/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEL133AK6--CGND-HRA-00013--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEL133AK6--CGND-HRA-00013--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZU200WEQ--CGND-HRA-00015--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZU200WEQ--CGND-HRA-00015--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEC006FND--CGND-HRA-00017--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEC006FND--CGND-HRA-00017--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKM699KKH--CGND-HRA-00018--Female--ALS_FTD--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKM699KKH--CGND-HRA-00018--Female--ALS_FTD--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWX086DGZ--CGND-HRA-00019--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWX086DGZ--CGND-HRA-00019--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXT979EZV--CGND-HRA-00022--Male--ALS_LB_FTD--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXT979EZV--CGND-HRA-00022--Male--ALS_LB_FTD--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEL133AK6--CGND-HRA-00027--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEL133AK6--CGND-HRA-00027--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYV496XLP--CGND-HRA-00028--Male--ALS_FTD_TM--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYV496XLP--CGND-HRA-00028--Male--ALS_FTD_TM--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZU200WEQ--CGND-HRA-00029--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZU200WEQ--CGND-HRA-00029--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEC006FND--CGND-HRA-00031--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEC006FND--CGND-HRA-00031--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKM699KKH--CGND-HRA-00032--Female--ALS_FTD--Spinal_Cord_Lumbar--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKM699KKH--CGND-HRA-00032--Female--ALS_FTD--Spinal_Cord_Lumbar--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJZ255ZC5--CGND-HRA-00034--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJZ255ZC5--CGND-HRA-00034--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXT979EZV--CGND-HRA-00036--Male--ALS_LB_FTD--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXT979EZV--CGND-HRA-00036--Male--ALS_LB_FTD--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEL133AK6--CGND-HRA-00041--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEL133AK6--CGND-HRA-00041--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYV496XLP--CGND-HRA-00042--Male--ALS_FTD_TM--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYV496XLP--CGND-HRA-00042--Male--ALS_FTD_TM--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZU200WEQ--CGND-HRA-00043--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZU200WEQ--CGND-HRA-00043--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEC006FND--CGND-HRA-00045--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEC006FND--CGND-HRA-00045--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKM699KKH--CGND-HRA-00046--Female--ALS_FTD--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKM699KKH--CGND-HRA-00046--Female--ALS_FTD--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWX086DGZ--CGND-HRA-00047--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWX086DGZ--CGND-HRA-00047--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJZ255ZC5--CGND-HRA-00048--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJZ255ZC5--CGND-HRA-00048--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXT979EZV--CGND-HRA-00050--Male--ALS_LB_FTD--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXT979EZV--CGND-HRA-00050--Male--ALS_LB_FTD--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEL133AK6--CGND-HRA-00055--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEL133AK6--CGND-HRA-00055--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYV496XLP--CGND-HRA-00056--Male--ALS_FTD_TM--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYV496XLP--CGND-HRA-00056--Male--ALS_FTD_TM--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZU200WEQ--CGND-HRA-00057--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZU200WEQ--CGND-HRA-00057--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEC006FND--CGND-HRA-00059--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEC006FND--CGND-HRA-00059--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKM699KKH--CGND-HRA-00060--Female--ALS_FTD--Cortex_Motor_Medial--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKM699KKH--CGND-HRA-00060--Female--ALS_FTD--Cortex_Motor_Medial--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWX086DGZ--CGND-HRA-00061--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWX086DGZ--CGND-HRA-00061--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJZ255ZC5--CGND-HRA-00062--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJZ255ZC5--CGND-HRA-00062--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXT979EZV--CGND-HRA-00064--Male--ALS_LB_FTD--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXT979EZV--CGND-HRA-00064--Male--ALS_LB_FTD--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEL133AK6--CGND-HRA-00069--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEL133AK6--CGND-HRA-00069--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYV496XLP--CGND-HRA-00070--Male--ALS_FTD_TM--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYV496XLP--CGND-HRA-00070--Male--ALS_FTD_TM--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZU200WEQ--CGND-HRA-00071--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZU200WEQ--CGND-HRA-00071--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEC006FND--CGND-HRA-00073--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEC006FND--CGND-HRA-00073--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKM699KKH--CGND-HRA-00074--Female--ALS_FTD--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKM699KKH--CGND-HRA-00074--Female--ALS_FTD--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWX086DGZ--CGND-HRA-00075--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWX086DGZ--CGND-HRA-00075--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJZ255ZC5--CGND-HRA-00076--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJZ255ZC5--CGND-HRA-00076--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXT979EZV--CGND-HRA-00078--Male--ALS_LB_FTD--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXT979EZV--CGND-HRA-00078--Male--ALS_LB_FTD--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEL133AK6--CGND-HRA-00083--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEL133AK6--CGND-HRA-00083--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZU200WEQ--CGND-HRA-00085--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZU200WEQ--CGND-HRA-00085--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEC006FND--CGND-HRA-00087--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEC006FND--CGND-HRA-00087--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKM699KKH--CGND-HRA-00088--Female--ALS_FTD--Cortex_Motor_Lateral--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKM699KKH--CGND-HRA-00088--Female--ALS_FTD--Cortex_Motor_Lateral--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJZ255ZC5--CGND-HRA-00090--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJZ255ZC5--CGND-HRA-00090--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXT979EZV--CGND-HRA-00092--Male--ALS_LB_FTD--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXT979EZV--CGND-HRA-00092--Male--ALS_LB_FTD--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU3--CGND-HRA-00099--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU3--CGND-HRA-00099--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU5--CGND-HRA-00101--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg_DCTN1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU5--CGND-HRA-00101--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg_DCTN1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU12--CGND-HRA-00108--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU12--CGND-HRA-00108--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU14--CGND-HRA-00110--Male--ALS--Cerebellum--C9orf72_neg_SOD1_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU14--CGND-HRA-00110--Male--ALS--Cerebellum--C9orf72_neg_SOD1_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU15--CGND-HRA-00111--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU15--CGND-HRA-00111--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUFT454ZFP--CGND-HRA-00203--Male--ALS--Cerebellum--C9orf72_neg_ANG_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUFT454ZFP--CGND-HRA-00203--Male--ALS--Cerebellum--C9orf72_neg_ANG_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMP035RP4--CGND-HRA-00204--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMP035RP4--CGND-HRA-00204--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDM397JGD--CGND-HRA-00205--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDM397JGD--CGND-HRA-00205--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHD481VCL--CGND-HRA-00206--Female--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHD481VCL--CGND-HRA-00206--Female--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDR086ZDQ--CGND-HRA-00207--Female--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDR086ZDQ--CGND-HRA-00207--Female--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG361GA9--CGND-HRA-00208--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG361GA9--CGND-HRA-00208--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUFT454ZFP--CGND-HRA-00209--Male--ALS--Cortex_Frontal--C9orf72_neg_ANG_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUFT454ZFP--CGND-HRA-00209--Male--ALS--Cortex_Frontal--C9orf72_neg_ANG_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMP035RP4--CGND-HRA-00210--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMP035RP4--CGND-HRA-00210--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDM397JGD--CGND-HRA-00211--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDM397JGD--CGND-HRA-00211--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHD481VCL--CGND-HRA-00212--Female--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHD481VCL--CGND-HRA-00212--Female--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDR086ZDQ--CGND-HRA-00213--Female--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDR086ZDQ--CGND-HRA-00213--Female--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG361GA9--CGND-HRA-00214--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG361GA9--CGND-HRA-00214--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUFT454ZFP--CGND-HRA-00215--Male--ALS--Cortex_Motor_Medial--C9orf72_neg_ANG_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUFT454ZFP--CGND-HRA-00215--Male--ALS--Cortex_Motor_Medial--C9orf72_neg_ANG_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMP035RP4--CGND-HRA-00216--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMP035RP4--CGND-HRA-00216--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDM397JGD--CGND-HRA-00217--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDM397JGD--CGND-HRA-00217--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHD481VCL--CGND-HRA-00218--Female--Non-Neurological_Control--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHD481VCL--CGND-HRA-00218--Female--Non-Neurological_Control--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDR086ZDQ--CGND-HRA-00219--Female--ALS--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDR086ZDQ--CGND-HRA-00219--Female--ALS--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG361GA9--CGND-HRA-00220--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG361GA9--CGND-HRA-00220--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUFT454ZFP--CGND-HRA-00221--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg_ANG_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUFT454ZFP--CGND-HRA-00221--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg_ANG_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMP035RP4--CGND-HRA-00222--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMP035RP4--CGND-HRA-00222--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDM397JGD--CGND-HRA-00223--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDM397JGD--CGND-HRA-00223--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHD481VCL--CGND-HRA-00224--Female--Non-Neurological_Control--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHD481VCL--CGND-HRA-00224--Female--Non-Neurological_Control--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDR086ZDQ--CGND-HRA-00225--Female--ALS--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDR086ZDQ--CGND-HRA-00225--Female--ALS--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG361GA9--CGND-HRA-00226--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG361GA9--CGND-HRA-00226--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUFT454ZFP--CGND-HRA-00227--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg_ANG_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUFT454ZFP--CGND-HRA-00227--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg_ANG_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMP035RP4--CGND-HRA-00228--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMP035RP4--CGND-HRA-00228--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDM397JGD--CGND-HRA-00229--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDM397JGD--CGND-HRA-00229--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHD481VCL--CGND-HRA-00230--Female--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHD481VCL--CGND-HRA-00230--Female--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDR086ZDQ--CGND-HRA-00231--Female--ALS--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDR086ZDQ--CGND-HRA-00231--Female--ALS--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG361GA9--CGND-HRA-00232--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG361GA9--CGND-HRA-00232--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUFT454ZFP--CGND-HRA-00233--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg_ANG_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUFT454ZFP--CGND-HRA-00233--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg_ANG_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMP035RP4--CGND-HRA-00234--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMP035RP4--CGND-HRA-00234--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDM397JGD--CGND-HRA-00235--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDM397JGD--CGND-HRA-00235--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHD481VCL--CGND-HRA-00236--Female--Non-Neurological_Control--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHD481VCL--CGND-HRA-00236--Female--Non-Neurological_Control--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDR086ZDQ--CGND-HRA-00237--Female--ALS--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDR086ZDQ--CGND-HRA-00237--Female--ALS--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG361GA9--CGND-HRA-00238--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG361GA9--CGND-HRA-00238--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNW210GCW--CGND-HRA-00054--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNW210GCW--CGND-HRA-00054--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNW210GCW--CGND-HRA-00068--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNW210GCW--CGND-HRA-00068--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHC282LVJ--CGND-HRA-00077--Female--Non-Neurological_Control--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHC282LVJ--CGND-HRA-00077--Female--Non-Neurological_Control--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNW210GCW--CGND-HRA-00082--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNW210GCW--CGND-HRA-00082--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWX086DGZ--CGND-HRA-00089-2--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWX086DGZ--CGND-HRA-00089-2--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHC282LVJ--CGND-HRA-00091--Female--Non-Neurological_Control--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHC282LVJ--CGND-HRA-00091--Female--Non-Neurological_Control--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNW210GCW--CGND-HRA-00096--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNW210GCW--CGND-HRA-00096--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU4--CGND-HRA-00100--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg_SETX_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU4--CGND-HRA-00100--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg_SETX_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU7--CGND-HRA-00103--Male--ALS--Liver--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU7--CGND-HRA-00103--Male--ALS--Liver--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU8--CGND-HRA-00104--Male--ALS--Cerebellum--C9orf72_neg_SOD1_pos_ALS2_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU8--CGND-HRA-00104--Male--ALS--Cerebellum--C9orf72_neg_SOD1_pos_ALS2_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU10--CGND-HRA-00106--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg_OPTN_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU10--CGND-HRA-00106--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg_OPTN_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU16--CGND-HRA-00112--Female--ALS--Liver--C9orf72_pos_SOD1_neg_NEK1_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU16--CGND-HRA-00112--Female--ALS--Liver--C9orf72_pos_SOD1_neg_NEK1_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU22--CGND-HRA-00118--Male--ALS--Cerebellum--C9orf72_pos_SOD1_neg_SPG11_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU22--CGND-HRA-00118--Male--ALS--Cerebellum--C9orf72_pos_SOD1_neg_SPG11_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU25--CGND-HRA-00121--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg_OPTN_pos_ANXA11_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU25--CGND-HRA-00121--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg_OPTN_pos_ANXA11_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU32--CGND-HRA-00128--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU32--CGND-HRA-00128--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU38--CGND-HRA-00134--Female--ALS--Cortex_Motor_Unspecified--C9orf72_pos_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU38--CGND-HRA-00134--Female--ALS--Cortex_Motor_Unspecified--C9orf72_pos_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU47--CGND-HRA-00143--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg_ANXA11_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU47--CGND-HRA-00143--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg_ANXA11_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU53--CGND-HRA-00149--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg_OPTN_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU53--CGND-HRA-00149--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg_OPTN_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU55--CGND-HRA-00151--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU55--CGND-HRA-00151--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU58--CGND-HRA-00154--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU58--CGND-HRA-00154--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU59--CGND-HRA-00155--Female--ALS--Liver--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU59--CGND-HRA-00155--Female--ALS--Liver--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU60--CGND-HRA-00156--Male--DLB_Peripheral_Neuropathy--Cerebellum--C9orf72_neg_SOD1_neg_NEFH_likely_benign_VAPB.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU60--CGND-HRA-00156--Male--DLB_Peripheral_Neuropathy--Cerebellum--C9orf72_neg_SOD1_neg_NEFH_likely_benign_VAPB.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU63--CGND-HRA-00159--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg_ALS2_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU63--CGND-HRA-00159--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg_ALS2_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU70--CGND-HRA-00166--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg_OPTN_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU70--CGND-HRA-00166--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg_OPTN_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU72--CGND-HRA-00168--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg_CCNF_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU72--CGND-HRA-00168--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg_CCNF_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU73--CGND-HRA-00169--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg_NEFH_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU73--CGND-HRA-00169--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg_NEFH_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU74--CGND-HRA-00170--Male--ALS--Cerebellum--C9orf72_neg_SOD1_pos_ANXA11_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU74--CGND-HRA-00170--Male--ALS--Cerebellum--C9orf72_neg_SOD1_pos_ANXA11_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU75--CGND-HRA-00171--Female--ALS--Spinal_Cord_Cervical--C9orf72_pos_SOD1_neg_OPTN_pos_SPG11_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU75--CGND-HRA-00171--Female--ALS--Spinal_Cord_Cervical--C9orf72_pos_SOD1_neg_OPTN_pos_SPG11_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU82--CGND-HRA-00178--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU82--CGND-HRA-00178--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU83--CGND-HRA-00179--Male--ALS--Cerebellum--C9orf72_neg_SOD1_pos_SPG11_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU83--CGND-HRA-00179--Male--ALS--Cerebellum--C9orf72_neg_SOD1_pos_SPG11_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKX037NKA--CGND-HRA-00182--Male--ALS_AD_FTD--Cerebellum--C9orf72_pos_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKX037NKA--CGND-HRA-00182--Male--ALS_AD_FTD--Cerebellum--C9orf72_pos_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAP156PM4--CGND-HRA-00183--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAP156PM4--CGND-HRA-00183--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMK638LUX--CGND-HRA-00188--Male--ALS--Liver--C9orf72_pos_SOD1_neg_ANXA11_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMK638LUX--CGND-HRA-00188--Male--ALS--Liver--C9orf72_pos_SOD1_neg_ANXA11_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURJ387PPV--CGND-HRA-00193--Female--ALS--Cortex_Motor_Unspecified--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURJ387PPV--CGND-HRA-00193--Female--ALS--Cortex_Motor_Unspecified--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUVB305VU7--CGND-HRA-00194--Male--ALS_AD_CTE--Cerebellum--SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUVB305VU7--CGND-HRA-00194--Male--ALS_AD_CTE--Cerebellum--SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTP414KZ2--CGND-HRA-00196--Female--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTP414KZ2--CGND-HRA-00196--Female--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUML172BXK--CGND-HRA-00197--Female--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUML172BXK--CGND-HRA-00197--Female--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEG442LDR--CGND-HRA-00199--Male--Non-Neurological_Control--Liver--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEG442LDR--CGND-HRA-00199--Male--Non-Neurological_Control--Liver--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZK186ZK4--CGND-HRA-00202--Female--ALS--Cerebellum--SOD1_neg_UBQLN2_pos_SPG11_NEK1_ANG.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZK186ZK4--CGND-HRA-00202--Female--ALS--Cerebellum--SOD1_neg_UBQLN2_pos_SPG11_NEK1_ANG.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKZ685AR4--CGND-HRA-00738--Female--Non-Neurological_Control--Cell_Line_Motor_Neuron--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKZ685AR4--CGND-HRA-00738--Female--Non-Neurological_Control--Cell_Line_Motor_Neuron--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKZ685AR4--CGND-HRA-00739--Female--Non-Neurological_Control--Cell_Line_iPS--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKZ685AR4--CGND-HRA-00739--Female--Non-Neurological_Control--Cell_Line_iPS--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-ATCC-BYS0112--CGND-HRA-00740--Male--Non-Neurological_Control--Cell_Line_iPS--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa ATCC-BYS0112--CGND-HRA-00740--Male--Non-Neurological_Control--Cell_Line_iPS--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-ATCC-BYS0112--CGND-HRA-00741--Male--Non-Neurological_Control--Cell_Line_Motor_Neuron--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa ATCC-BYS0112--CGND-HRA-00741--Male--Non-Neurological_Control--Cell_Line_Motor_Neuron--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-ATCC-BXS0114--CGND-HRA-00742--Female--Non-Neurological_Control--Cell_Line_iPS--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa ATCC-BXS0114--CGND-HRA-00742--Female--Non-Neurological_Control--Cell_Line_iPS--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-ATCC-BXS0114--CGND-HRA-00743--Female--Non-Neurological_Control--Cell_Line_Motor_Neuron--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa ATCC-BXS0114--CGND-HRA-00743--Female--Non-Neurological_Control--Cell_Line_Motor_Neuron--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUVU845ZAB--CGND-HRA-00744--Female--ALS--Cell_Line_iPS--SOD1_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUVU845ZAB--CGND-HRA-00744--Female--ALS--Cell_Line_iPS--SOD1_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUVU845ZAB--CGND-HRA-00745--Female--ALS--Cell_Line_Motor_Neuron--SOD1_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUVU845ZAB--CGND-HRA-00745--Female--ALS--Cell_Line_Motor_Neuron--SOD1_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHM340FBZ--CGND-HRA-00706--Male--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHM340FBZ--CGND-HRA-00706--Male--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNY116EZW--CGND-HRA-00713--Female--ALS_NOS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNY116EZW--CGND-HRA-00713--Female--ALS_NOS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXD817GGZ--CGND-HRA-00718--Male--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXD817GGZ--CGND-HRA-00718--Male--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEULT268RM4--CGND-HRA-00719--Male--ALS_FTD--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEULT268RM4--CGND-HRA-00719--Male--ALS_FTD--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURN516YR8--CGND-HRA-00720--Female--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURN516YR8--CGND-HRA-00720--Female--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURD711XCL--CGND-HRA-00721--Female--Pre-fALS--Cerebellum--ANG_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURD711XCL--CGND-HRA-00721--Female--Pre-fALS--Cerebellum--ANG_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUCV649UJK--CGND-HRA-00722--Male--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUCV649UJK--CGND-HRA-00722--Male--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUE532LFF--CGND-HRA-00723--Male--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUE532LFF--CGND-HRA-00723--Male--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYY221HZA--CGND-HRA-00724--Male--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYY221HZA--CGND-HRA-00724--Male--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUPK732LNT--CGND-HRA-00725--Female--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUPK732LNT--CGND-HRA-00725--Female--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEULH901PYF--CGND-HRA-00726--Male--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEULH901PYF--CGND-HRA-00726--Male--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUCW292DYJ--CGND-HRA-00727--Female--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUCW292DYJ--CGND-HRA-00727--Female--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXT258BD4--CGND-HRA-00728--Female--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXT258BD4--CGND-HRA-00728--Female--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURK749WFB--CGND-HRA-00729--Female--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURK749WFB--CGND-HRA-00729--Female--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNL548ZBN--CGND-HRA-00730--Male--ALS_FTD--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNL548ZBN--CGND-HRA-00730--Male--ALS_FTD--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYV496XLP--CGND-HRA-00014-2--Male--ALS_FTD_TM--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYV496XLP--CGND-HRA-00014-2--Male--ALS_FTD_TM--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUME287RK2--CGND-HRA-00016--Female--ALS_FTD--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUME287RK2--CGND-HRA-00016--Female--ALS_FTD--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJZ255ZC5--CGND-HRA-00020-2--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJZ255ZC5--CGND-HRA-00020-2--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHC282LVJ--CGND-HRA-00021--Female--Non-Neurological_Control--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHC282LVJ--CGND-HRA-00021--Female--Non-Neurological_Control--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYB686REL--CGND-HRA-00023--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYB686REL--CGND-HRA-00023--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJR139GPF--CGND-HRA-00024--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJR139GPF--CGND-HRA-00024--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGA773REC--CGND-HRA-00025--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGA773REC--CGND-HRA-00025--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNW210GCW--CGND-HRA-00026--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNW210GCW--CGND-HRA-00026--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHC282LVJ--CGND-HRA-00035--Female--Non-Neurological_Control--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHC282LVJ--CGND-HRA-00035--Female--Non-Neurological_Control--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYB686REL--CGND-HRA-00037--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYB686REL--CGND-HRA-00037--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJR139GPF--CGND-HRA-00038--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJR139GPF--CGND-HRA-00038--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGA773REC--CGND-HRA-00039--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGA773REC--CGND-HRA-00039--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNW210GCW--CGND-HRA-00040--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNW210GCW--CGND-HRA-00040--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHC282LVJ--CGND-HRA-00049--Female--Non-Neurological_Control--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHC282LVJ--CGND-HRA-00049--Female--Non-Neurological_Control--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYB686REL--CGND-HRA-00051--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYB686REL--CGND-HRA-00051--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJR139GPF--CGND-HRA-00052--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJR139GPF--CGND-HRA-00052--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGA773REC--CGND-HRA-00053--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGA773REC--CGND-HRA-00053--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUME287RK2--CGND-HRA-00058--Female--ALS_FTD--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUME287RK2--CGND-HRA-00058--Female--ALS_FTD--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHC282LVJ--CGND-HRA-00063--Female--Non-Neurological_Control--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHC282LVJ--CGND-HRA-00063--Female--Non-Neurological_Control--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYB686REL--CGND-HRA-00065--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYB686REL--CGND-HRA-00065--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJR139GPF--CGND-HRA-00066--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJR139GPF--CGND-HRA-00066--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUME287RK2--CGND-HRA-00072--Female--ALS_FTD--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUME287RK2--CGND-HRA-00072--Female--ALS_FTD--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYB686REL--CGND-HRA-00079--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYB686REL--CGND-HRA-00079--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGA773REC--CGND-HRA-00081--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGA773REC--CGND-HRA-00081--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYV496XLP--CGND-HRA-00084-2--Male--ALS_FTD_TM--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYV496XLP--CGND-HRA-00084-2--Male--ALS_FTD_TM--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUME287RK2--CGND-HRA-00086--Female--ALS_FTD--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUME287RK2--CGND-HRA-00086--Female--ALS_FTD--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYB686REL--CGND-HRA-00093--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYB686REL--CGND-HRA-00093--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGA773REC--CGND-HRA-00095--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGA773REC--CGND-HRA-00095--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU28--CGND-HRA-00124--Male--ALS--Cortex_Sensory--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU28--CGND-HRA-00124--Male--ALS--Cortex_Sensory--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU30--CGND-HRA-00126--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU30--CGND-HRA-00126--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU33--CGND-HRA-00129--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_negMATR3_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU33--CGND-HRA-00129--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_negMATR3_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU43--CGND-HRA-00139--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU43--CGND-HRA-00139--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU52--CGND-HRA-00148--Male--ALS--Cortex_Frontal--C9orf72_pos_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU52--CGND-HRA-00148--Male--ALS--Cortex_Frontal--C9orf72_pos_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU57--CGND-HRA-00153--Male--ALS--Liver--C9orf72_neg_SOD1_neg_FUS_pos_ALS2_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU57--CGND-HRA-00153--Male--ALS--Liver--C9orf72_neg_SOD1_neg_FUS_pos_ALS2_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU64--CGND-HRA-00160--Male--ALS_FTD--Cortex_Frontal--C9orf72_neg_SOD1_neg_NEK1_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU64--CGND-HRA-00160--Male--ALS_FTD--Cortex_Frontal--C9orf72_neg_SOD1_neg_NEK1_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-GWF14-01--CGND-HRA-00295--Female--Pre-fALS_FTD--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa GWF14-01--CGND-HRA-00295--Female--Pre-fALS_FTD--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-GWF14-01--CGND-HRA-00296--Female--Pre-fALS_FTD--Cortex_Motor_Medial--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa GWF14-01--CGND-HRA-00296--Female--Pre-fALS_FTD--Cortex_Motor_Medial--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-GWF14-01--CGND-HRA-00297--Female--Pre-fALS_FTD--Cortex_Motor_Lateral--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa GWF14-01--CGND-HRA-00297--Female--Pre-fALS_FTD--Cortex_Motor_Lateral--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-GWF14-01--CGND-HRA-00298--Female--Pre-fALS_FTD--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa GWF14-01--CGND-HRA-00298--Female--Pre-fALS_FTD--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-GWF14-01--CGND-HRA-00299--Female--Pre-fALS_FTD--Spinal_Cord_Lumbar--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa GWF14-01--CGND-HRA-00299--Female--Pre-fALS_FTD--Spinal_Cord_Lumbar--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-GWF14-01--CGND-HRA-00300--Female--Pre-fALS_FTD--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa GWF14-01--CGND-HRA-00300--Female--Pre-fALS_FTD--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-GWF14-01--CGND-HRA-00301--Female--Pre-fALS_FTD--Cortex_Occipital--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa GWF14-01--CGND-HRA-00301--Female--Pre-fALS_FTD--Cortex_Occipital--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-GWF14-01--CGND-HRA-00302--Female--Pre-fALS_FTD--Spinal_Cord_Thoracic--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa GWF14-01--CGND-HRA-00302--Female--Pre-fALS_FTD--Spinal_Cord_Thoracic--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEF397VVN--CGND-HRA-00303--Female--ALS_AD--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEF397VVN--CGND-HRA-00303--Female--ALS_AD--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEF397VVN--CGND-HRA-00304--Female--ALS_AD--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEF397VVN--CGND-HRA-00304--Female--ALS_AD--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEF397VVN--CGND-HRA-00305--Female--ALS_AD--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEF397VVN--CGND-HRA-00305--Female--ALS_AD--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEF397VVN--CGND-HRA-00306--Female--ALS_AD--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEF397VVN--CGND-HRA-00306--Female--ALS_AD--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEF397VVN--CGND-HRA-00307--Female--ALS_AD--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEF397VVN--CGND-HRA-00307--Female--ALS_AD--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEF397VVN--CGND-HRA-00308--Female--ALS_AD--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEF397VVN--CGND-HRA-00308--Female--ALS_AD--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEF397VVN--CGND-HRA-00309--Female--ALS_AD--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEF397VVN--CGND-HRA-00309--Female--ALS_AD--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEF397VVN--CGND-HRA-00310--Female--ALS_AD--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEF397VVN--CGND-HRA-00310--Female--ALS_AD--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWZ373ZHA--CGND-HRA-00311--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWZ373ZHA--CGND-HRA-00311--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWZ373ZHA--CGND-HRA-00312--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWZ373ZHA--CGND-HRA-00312--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWZ373ZHA--CGND-HRA-00313--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWZ373ZHA--CGND-HRA-00313--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWZ373ZHA--CGND-HRA-00314--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWZ373ZHA--CGND-HRA-00314--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWZ373ZHA--CGND-HRA-00315--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWZ373ZHA--CGND-HRA-00315--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWZ373ZHA--CGND-HRA-00316--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWZ373ZHA--CGND-HRA-00316--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWZ373ZHA--CGND-HRA-00317--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWZ373ZHA--CGND-HRA-00317--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWZ373ZHA--CGND-HRA-00318--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWZ373ZHA--CGND-HRA-00318--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTL441LZ7--CGND-HRA-00319--Male--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTL441LZ7--CGND-HRA-00319--Male--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTL441LZ7--CGND-HRA-00320--Male--ALS--Cortex_Motor_Medial--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTL441LZ7--CGND-HRA-00320--Male--ALS--Cortex_Motor_Medial--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTL441LZ7--CGND-HRA-00321--Male--ALS--Cortex_Motor_Lateral--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTL441LZ7--CGND-HRA-00321--Male--ALS--Cortex_Motor_Lateral--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTL441LZ7--CGND-HRA-00323--Male--ALS--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTL441LZ7--CGND-HRA-00323--Male--ALS--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTL441LZ7--CGND-HRA-00324--Male--ALS--Cortex_Occipital--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTL441LZ7--CGND-HRA-00324--Male--ALS--Cortex_Occipital--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTL441LZ7--CGND-HRA-00325--Male--ALS--Spinal_Cord_Thoracic--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTL441LZ7--CGND-HRA-00325--Male--ALS--Spinal_Cord_Thoracic--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUVZ387WGH--CGND-HRA-00326--Female--ALS_AD--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUVZ387WGH--CGND-HRA-00326--Female--ALS_AD--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUVZ387WGH--CGND-HRA-00328--Female--ALS_AD--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUVZ387WGH--CGND-HRA-00328--Female--ALS_AD--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUVZ387WGH--CGND-HRA-00330--Female--ALS_AD--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUVZ387WGH--CGND-HRA-00330--Female--ALS_AD--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUVZ387WGH--CGND-HRA-00331--Female--ALS_AD--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUVZ387WGH--CGND-HRA-00331--Female--ALS_AD--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAT369TG5--CGND-HRA-00333--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAT369TG5--CGND-HRA-00333--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAT369TG5--CGND-HRA-00334--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAT369TG5--CGND-HRA-00334--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAT369TG5--CGND-HRA-00335--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAT369TG5--CGND-HRA-00335--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAT369TG5--CGND-HRA-00336--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAT369TG5--CGND-HRA-00336--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAT369TG5--CGND-HRA-00338--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAT369TG5--CGND-HRA-00338--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAT369TG5--CGND-HRA-00340--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAT369TG5--CGND-HRA-00340--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAV667LJK--CGND-HRA-00341--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAV667LJK--CGND-HRA-00341--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAV667LJK--CGND-HRA-00342--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAV667LJK--CGND-HRA-00342--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAV667LJK--CGND-HRA-00343--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAV667LJK--CGND-HRA-00343--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAV667LJK--CGND-HRA-00344--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAV667LJK--CGND-HRA-00344--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAV667LJK--CGND-HRA-00345--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAV667LJK--CGND-HRA-00345--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAV667LJK--CGND-HRA-00346--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAV667LJK--CGND-HRA-00346--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAV667LJK--CGND-HRA-00347--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAV667LJK--CGND-HRA-00347--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAV667LJK--CGND-HRA-00348--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAV667LJK--CGND-HRA-00348--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNW244GF0--CGND-HRA-00350--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNW244GF0--CGND-HRA-00350--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNW244GF0--CGND-HRA-00352--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNW244GF0--CGND-HRA-00352--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNW244GF0--CGND-HRA-00353--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNW244GF0--CGND-HRA-00353--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKY135CV6--CGND-HRA-00380--Male--ALS_AD--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKY135CV6--CGND-HRA-00380--Male--ALS_AD--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKY135CV6--CGND-HRA-00381--Male--ALS_AD--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKY135CV6--CGND-HRA-00381--Male--ALS_AD--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKY135CV6--CGND-HRA-00382--Male--ALS_AD--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKY135CV6--CGND-HRA-00382--Male--ALS_AD--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKY135CV6--CGND-HRA-00383--Male--ALS_AD--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKY135CV6--CGND-HRA-00383--Male--ALS_AD--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKY135CV6--CGND-HRA-00384--Male--ALS_AD--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKY135CV6--CGND-HRA-00384--Male--ALS_AD--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKY135CV6--CGND-HRA-00385--Male--ALS_AD--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKY135CV6--CGND-HRA-00385--Male--ALS_AD--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYX020CB0--CGND-HRA-00386--Male--ALS_AD--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYX020CB0--CGND-HRA-00386--Male--ALS_AD--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYX020CB0--CGND-HRA-00387--Male--ALS_AD--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYX020CB0--CGND-HRA-00387--Male--ALS_AD--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYX020CB0--CGND-HRA-00388--Male--ALS_AD--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYX020CB0--CGND-HRA-00388--Male--ALS_AD--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAT369TG5--CGND-HRA-00339--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAT369TG5--CGND-HRA-00339--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNW244GF0--CGND-HRA-00349--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNW244GF0--CGND-HRA-00349--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNW244GF0--CGND-HRA-00351--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNW244GF0--CGND-HRA-00351--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNW244GF0--CGND-HRA-00354--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNW244GF0--CGND-HRA-00354--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNW244GF0--CGND-HRA-00355--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNW244GF0--CGND-HRA-00355--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNW244GF0--CGND-HRA-00356--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNW244GF0--CGND-HRA-00356--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTP019MY9--CGND-HRA-00357--Female--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTP019MY9--CGND-HRA-00357--Female--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTP019MY9--CGND-HRA-00358--Female--ALS--Cortex_Motor_Medial--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTP019MY9--CGND-HRA-00358--Female--ALS--Cortex_Motor_Medial--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTP019MY9--CGND-HRA-00359--Female--ALS--Cortex_Motor_Lateral--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTP019MY9--CGND-HRA-00359--Female--ALS--Cortex_Motor_Lateral--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTP019MY9--CGND-HRA-00360--Female--ALS--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTP019MY9--CGND-HRA-00360--Female--ALS--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTP019MY9--CGND-HRA-00361--Female--ALS--Spinal_Cord_Lumbar--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTP019MY9--CGND-HRA-00361--Female--ALS--Spinal_Cord_Lumbar--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTP019MY9--CGND-HRA-00362--Female--ALS--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTP019MY9--CGND-HRA-00362--Female--ALS--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTP019MY9--CGND-HRA-00363--Female--ALS--Cortex_Occipital--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTP019MY9--CGND-HRA-00363--Female--ALS--Cortex_Occipital--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGV399KJW--CGND-HRA-00365--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGV399KJW--CGND-HRA-00365--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGV399KJW--CGND-HRA-00366--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGV399KJW--CGND-HRA-00366--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGV399KJW--CGND-HRA-00367--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGV399KJW--CGND-HRA-00367--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGV399KJW--CGND-HRA-00368--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGV399KJW--CGND-HRA-00368--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGV399KJW--CGND-HRA-00369--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGV399KJW--CGND-HRA-00369--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGV399KJW--CGND-HRA-00370--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGV399KJW--CGND-HRA-00370--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZX073BDK--CGND-HRA-00372--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZX073BDK--CGND-HRA-00372--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZX073BDK--CGND-HRA-00373--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZX073BDK--CGND-HRA-00373--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZX073BDK--CGND-HRA-00374--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZX073BDK--CGND-HRA-00374--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZX073BDK--CGND-HRA-00375--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZX073BDK--CGND-HRA-00375--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZX073BDK--CGND-HRA-00376--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZX073BDK--CGND-HRA-00376--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYX020CB0--CGND-HRA-00389--Male--ALS_AD--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYX020CB0--CGND-HRA-00389--Male--ALS_AD--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYX020CB0--CGND-HRA-00390--Male--ALS_AD--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYX020CB0--CGND-HRA-00390--Male--ALS_AD--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYX020CB0--CGND-HRA-00391--Male--ALS_AD--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYX020CB0--CGND-HRA-00391--Male--ALS_AD--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMT947ALA--CGND-HRA-00392--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMT947ALA--CGND-HRA-00392--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMT947ALA--CGND-HRA-00393--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMT947ALA--CGND-HRA-00393--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMT947ALA--CGND-HRA-00394--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMT947ALA--CGND-HRA-00394--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMT947ALA--CGND-HRA-00395--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMT947ALA--CGND-HRA-00395--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMT947ALA--CGND-HRA-00396--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMT947ALA--CGND-HRA-00396--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMT947ALA--CGND-HRA-00397--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMT947ALA--CGND-HRA-00397--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNE940RZC--CGND-HRA-00398--Male--AD--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNE940RZC--CGND-HRA-00398--Male--AD--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNE940RZC--CGND-HRA-00399--Male--AD--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNE940RZC--CGND-HRA-00399--Male--AD--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNE940RZC--CGND-HRA-00400--Male--AD--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNE940RZC--CGND-HRA-00400--Male--AD--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNE940RZC--CGND-HRA-00401--Male--AD--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNE940RZC--CGND-HRA-00401--Male--AD--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNE940RZC--CGND-HRA-00402--Male--AD--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNE940RZC--CGND-HRA-00402--Male--AD--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNE940RZC--CGND-HRA-00403--Male--AD--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNE940RZC--CGND-HRA-00403--Male--AD--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEE593VY7--CGND-HRA-00404--Male--MSA--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEE593VY7--CGND-HRA-00404--Male--MSA--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEE593VY7--CGND-HRA-00405--Male--MSA--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEE593VY7--CGND-HRA-00405--Male--MSA--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEE593VY7--CGND-HRA-00406--Male--MSA--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEE593VY7--CGND-HRA-00406--Male--MSA--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEE593VY7--CGND-HRA-00407--Male--MSA--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEE593VY7--CGND-HRA-00407--Male--MSA--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEE593VY7--CGND-HRA-00408--Male--MSA--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEE593VY7--CGND-HRA-00408--Male--MSA--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEE593VY7--CGND-HRA-00409--Male--MSA--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEE593VY7--CGND-HRA-00409--Male--MSA--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMV641VYK--CGND-HRA-00410--Male--AD--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMV641VYK--CGND-HRA-00410--Male--AD--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMV641VYK--CGND-HRA-00411--Male--AD--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMV641VYK--CGND-HRA-00411--Male--AD--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMV641VYK--CGND-HRA-00412--Male--AD--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMV641VYK--CGND-HRA-00412--Male--AD--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMV641VYK--CGND-HRA-00414--Male--AD--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMV641VYK--CGND-HRA-00414--Male--AD--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTZ062XC5--CGND-HRA-00653--Male--SBMA--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTZ062XC5--CGND-HRA-00653--Male--SBMA--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTZ062XC5--CGND-HRA-00654--Male--SBMA--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTZ062XC5--CGND-HRA-00654--Male--SBMA--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTZ062XC5--CGND-HRA-00655--Male--SBMA--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTZ062XC5--CGND-HRA-00655--Male--SBMA--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTZ062XC5--CGND-HRA-00656--Male--SBMA--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTZ062XC5--CGND-HRA-00656--Male--SBMA--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTZ062XC5--CGND-HRA-00657--Male--SBMA--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTZ062XC5--CGND-HRA-00657--Male--SBMA--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU56--CGND-HRA-00152--Male--ALS--Liver--C9orf72_neg_SOD1_neg_TARDBP_pos_TBK1_ALS2_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU56--CGND-HRA-00152--Male--ALS--Liver--C9orf72_neg_SOD1_neg_TARDBP_pos_TBK1_ALS2_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU79--CGND-HRA-00175--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU79--CGND-HRA-00175--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTZ062XC5--CGND-HRA-00195--Male--SBMA--Liver--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTZ062XC5--CGND-HRA-00195--Male--SBMA--Liver--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXY076JMB--CGND-HRA-00198--Female--ALS--Liver--SOD1_neg_FIG4_pos_SETX.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXY076JMB--CGND-HRA-00198--Female--ALS--Liver--SOD1_neg_FIG4_pos_SETX.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNJ406FRR--CGND-HRA-00270--Female--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNJ406FRR--CGND-HRA-00270--Female--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURK749WFB--CGND-HRA-00277--Female--ALS--Spinal_Cord_Lumbar--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURK749WFB--CGND-HRA-00277--Female--ALS--Spinal_Cord_Lumbar--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXR099CKK--CGND-HRA-00282--Female--Non-Neurological_Control--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXR099CKK--CGND-HRA-00282--Female--Non-Neurological_Control--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZX073BDK--CGND-HRA-00377--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZX073BDK--CGND-HRA-00377--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZX073BDK--CGND-HRA-00378--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZX073BDK--CGND-HRA-00378--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZX073BDK--CGND-HRA-00379--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZX073BDK--CGND-HRA-00379--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMV641VYK--CGND-HRA-00413--Male--AD--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMV641VYK--CGND-HRA-00413--Male--AD--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMV641VYK--CGND-HRA-00415--Male--AD--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMV641VYK--CGND-HRA-00415--Male--AD--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWP285RM6--CGND-HRA-00416--Female--ALS_AD--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWP285RM6--CGND-HRA-00416--Female--ALS_AD--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWP285RM6--CGND-HRA-00417--Female--ALS_AD--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWP285RM6--CGND-HRA-00417--Female--ALS_AD--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWP285RM6--CGND-HRA-00418--Female--ALS_AD--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWP285RM6--CGND-HRA-00418--Female--ALS_AD--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWP285RM6--CGND-HRA-00419--Female--ALS_AD--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWP285RM6--CGND-HRA-00419--Female--ALS_AD--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWP285RM6--CGND-HRA-00420--Female--ALS_AD--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWP285RM6--CGND-HRA-00420--Female--ALS_AD--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWP285RM6--CGND-HRA-00421--Female--ALS_AD--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWP285RM6--CGND-HRA-00421--Female--ALS_AD--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDT233ZZ1--CGND-HRA-00422--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDT233ZZ1--CGND-HRA-00422--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDT233ZZ1--CGND-HRA-00423--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDT233ZZ1--CGND-HRA-00423--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDT233ZZ1--CGND-HRA-00424--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDT233ZZ1--CGND-HRA-00424--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDT233ZZ1--CGND-HRA-00425--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDT233ZZ1--CGND-HRA-00425--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDT233ZZ1--CGND-HRA-00426--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDT233ZZ1--CGND-HRA-00426--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDT233ZZ1--CGND-HRA-00427--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDT233ZZ1--CGND-HRA-00427--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG727NTW--CGND-HRA-00428--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG727NTW--CGND-HRA-00428--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG727NTW--CGND-HRA-00429--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG727NTW--CGND-HRA-00429--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG727NTW--CGND-HRA-00430--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG727NTW--CGND-HRA-00430--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG727NTW--CGND-HRA-00431--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG727NTW--CGND-HRA-00431--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG727NTW--CGND-HRA-00432--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG727NTW--CGND-HRA-00432--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG727NTW--CGND-HRA-00433--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG727NTW--CGND-HRA-00433--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTB398FC9--CGND-HRA-00434--Male--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTB398FC9--CGND-HRA-00434--Male--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTB398FC9--CGND-HRA-00435--Male--ALS--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTB398FC9--CGND-HRA-00435--Male--ALS--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTB398FC9--CGND-HRA-00436--Male--ALS--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTB398FC9--CGND-HRA-00436--Male--ALS--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTB398FC9--CGND-HRA-00437--Male--ALS--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTB398FC9--CGND-HRA-00437--Male--ALS--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTB398FC9--CGND-HRA-00438--Male--ALS--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTB398FC9--CGND-HRA-00438--Male--ALS--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTB398FC9--CGND-HRA-00439--Male--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTB398FC9--CGND-HRA-00439--Male--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURD711XCL--CGND-HRA-00242--Female--Pre-fALS--Cortex_Frontal--ANG_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURD711XCL--CGND-HRA-00242--Female--Pre-fALS--Cortex_Frontal--ANG_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUE532LFF--CGND-HRA-00250--Male--ALS--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUE532LFF--CGND-HRA-00250--Male--ALS--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURD711XCL--CGND-HRA-00251--Female--Pre-fALS--Cortex_Motor_Medial--ANG_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURD711XCL--CGND-HRA-00251--Female--Pre-fALS--Cortex_Motor_Medial--ANG_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUCV649UJK--CGND-HRA-00252--Male--ALS--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUCV649UJK--CGND-HRA-00252--Male--ALS--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURK749WFB--CGND-HRA-00254--Female--ALS--Cortex_Motor_Medial--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURK749WFB--CGND-HRA-00254--Female--ALS--Cortex_Motor_Medial--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUE532LFF--CGND-HRA-00260--Male--ALS--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUE532LFF--CGND-HRA-00260--Male--ALS--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURD711XCL--CGND-HRA-00261--Female--Pre-fALS--Spinal_Cord_Cervical--ANG_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURD711XCL--CGND-HRA-00261--Female--Pre-fALS--Spinal_Cord_Cervical--ANG_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUCV649UJK--CGND-HRA-00262--Male--ALS--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUCV649UJK--CGND-HRA-00262--Male--ALS--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURK749WFB--CGND-HRA-00264--Female--ALS--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURK749WFB--CGND-HRA-00264--Female--ALS--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYY221HZA--CGND-HRA-00272--Male--ALS--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYY221HZA--CGND-HRA-00272--Male--ALS--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUCV649UJK--CGND-HRA-00275--Male--ALS--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUCV649UJK--CGND-HRA-00275--Male--ALS--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNL548ZBN--CGND-HRA-00276--Male--ALS_FTD--Spinal_Cord_Lumbar--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNL548ZBN--CGND-HRA-00276--Male--ALS_FTD--Spinal_Cord_Lumbar--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYY221HZA--CGND-HRA-00284--Male--ALS--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYY221HZA--CGND-HRA-00284--Male--ALS--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUE532LFF--CGND-HRA-00285--Male--ALS--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUE532LFF--CGND-HRA-00285--Male--ALS--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXT258BD4--CGND-HRA-00288--Female--ALS--Cortex_Motor_Unspecified--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXT258BD4--CGND-HRA-00288--Female--ALS--Cortex_Motor_Unspecified--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAT369TG5--CGND-HRA-00337--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAT369TG5--CGND-HRA-00337--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTP019MY9--CGND-HRA-00364--Female--ALS--Spinal_Cord_Thoracic--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTP019MY9--CGND-HRA-00364--Female--ALS--Spinal_Cord_Thoracic--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEH612JPA--CGND-HRA-00612--Female--ALS_AD--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEH612JPA--CGND-HRA-00612--Female--ALS_AD--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUE532LFF--CGND-HRA-00241--Male--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUE532LFF--CGND-HRA-00241--Male--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURK749WFB--CGND-HRA-00245--Female--ALS--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURK749WFB--CGND-HRA-00245--Female--ALS--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUPK732LNT--CGND-HRA-00246--Female--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUPK732LNT--CGND-HRA-00246--Female--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUCW292DYJ--CGND-HRA-00247--Female--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUCW292DYJ--CGND-HRA-00247--Female--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEULH901PYF--CGND-HRA-00248--Male--ALS--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEULH901PYF--CGND-HRA-00248--Male--ALS--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUPK732LNT--CGND-HRA-00255--Female--ALS--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUPK732LNT--CGND-HRA-00255--Female--ALS--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUCW292DYJ--CGND-HRA-00256--Female--ALS--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUCW292DYJ--CGND-HRA-00256--Female--ALS--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXT258BD4--CGND-HRA-00258--Female--ALS--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXT258BD4--CGND-HRA-00258--Female--ALS--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYY221HZA--CGND-HRA-00259--Male--ALS--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYY221HZA--CGND-HRA-00259--Male--ALS--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNL548ZBN--CGND-HRA-00263--Male--ALS_FTD--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNL548ZBN--CGND-HRA-00263--Male--ALS_FTD--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUPK732LNT--CGND-HRA-00265--Female--ALS--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUPK732LNT--CGND-HRA-00265--Female--ALS--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUCW292DYJ--CGND-HRA-00266--Female--ALS--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUCW292DYJ--CGND-HRA-00266--Female--ALS--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEULH901PYF--CGND-HRA-00267--Male--ALS--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEULH901PYF--CGND-HRA-00267--Male--ALS--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEULM733WR7--CGND-HRA-00268--Female--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEULM733WR7--CGND-HRA-00268--Female--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXR099CKK--CGND-HRA-00269--Female--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXR099CKK--CGND-HRA-00269--Female--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUCW292DYJ--CGND-HRA-00279--Female--ALS--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUCW292DYJ--CGND-HRA-00279--Female--ALS--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEULH901PYF--CGND-HRA-00280--Male--ALS--Spinal_Cord_Lumbar--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEULH901PYF--CGND-HRA-00280--Male--ALS--Spinal_Cord_Lumbar--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEULM733WR7--CGND-HRA-00281--Female--Non-Neurological_Control--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEULM733WR7--CGND-HRA-00281--Female--Non-Neurological_Control--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNJ406FRR--CGND-HRA-00283--Female--Non-Neurological_Control--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNJ406FRR--CGND-HRA-00283--Female--Non-Neurological_Control--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNL548ZBN--CGND-HRA-00286--Male--ALS_FTD--Cortex_Motor_Lateral--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNL548ZBN--CGND-HRA-00286--Male--ALS_FTD--Cortex_Motor_Lateral--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEULH901PYF--CGND-HRA-00287--Male--ALS--Cortex_Motor_Lateral--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEULH901PYF--CGND-HRA-00287--Male--ALS--Cortex_Motor_Lateral--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU73--CGND-HRA-00523--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg_NEFH_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU73--CGND-HRA-00523--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg_NEFH_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU79--CGND-HRA-00525--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU79--CGND-HRA-00525--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU79--CGND-HRA-00526--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU79--CGND-HRA-00526--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU79--CGND-HRA-00527--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU79--CGND-HRA-00527--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU79--CGND-HRA-00528--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU79--CGND-HRA-00528--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU80--CGND-HRA-00529--Female--PLS--Cortex_Frontal--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU80--CGND-HRA-00529--Female--PLS--Cortex_Frontal--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU80--CGND-HRA-00530--Female--PLS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU80--CGND-HRA-00530--Female--PLS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU73--CGND-HRA-00553--Female--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg_NEFH_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU73--CGND-HRA-00553--Female--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg_NEFH_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU73--CGND-HRA-00554--Female--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg_NEFH_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU73--CGND-HRA-00554--Female--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg_NEFH_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU74--CGND-HRA-00559--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_pos_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU74--CGND-HRA-00559--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_pos_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU74--CGND-HRA-00560--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_pos_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU74--CGND-HRA-00560--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_pos_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU79--CGND-HRA-00563--Male--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU79--CGND-HRA-00563--Male--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU79--CGND-HRA-00564--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU79--CGND-HRA-00564--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU79--CGND-HRA-00565--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU79--CGND-HRA-00565--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU80--CGND-HRA-00566--Female--PLS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU80--CGND-HRA-00566--Female--PLS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU80--CGND-HRA-00567--Female--PLS--Cortex_Occipital--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU80--CGND-HRA-00567--Female--PLS--Cortex_Occipital--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU80--CGND-HRA-00568--Female--PLS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU80--CGND-HRA-00568--Female--PLS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU80--CGND-HRA-00569--Female--PLS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU80--CGND-HRA-00569--Female--PLS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU80--CGND-HRA-00570--Female--PLS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU80--CGND-HRA-00570--Female--PLS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU82--CGND-HRA-00531--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU82--CGND-HRA-00531--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU83--CGND-HRA-00532--Male--ALS--Cerebellum--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU83--CGND-HRA-00532--Male--ALS--Cerebellum--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKX037NKA--CGND-HRA-00533--Male--ALS_AD_FTD--Cerebellum--C9orf72_pos_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKX037NKA--CGND-HRA-00533--Male--ALS_AD_FTD--Cerebellum--C9orf72_pos_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAP156PM4--CGND-HRA-00534--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAP156PM4--CGND-HRA-00534--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAP156PM4--CGND-HRA-00535--Female--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAP156PM4--CGND-HRA-00535--Female--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAP156PM4--CGND-HRA-00536--Female--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAP156PM4--CGND-HRA-00536--Female--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUW911LWA--CGND-HRA-00538--Male--ALS_FTD--Cerebellum--C9orf72_pos_SOD1_neg_NEFH_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUW911LWA--CGND-HRA-00538--Male--ALS_FTD--Cerebellum--C9orf72_pos_SOD1_neg_NEFH_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUW911LWA--CGND-HRA-00540--Male--ALS_FTD--Cortex_Occipital--C9orf72_pos_SOD1_neg_NEFH_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUW911LWA--CGND-HRA-00540--Male--ALS_FTD--Cortex_Occipital--C9orf72_pos_SOD1_neg_NEFH_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEH612JPA--CGND-HRA-00542--Female--ALS_AD--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEH612JPA--CGND-HRA-00542--Female--ALS_AD--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEH612JPA--CGND-HRA-00543--Female--ALS_AD--Cortex_Frontal--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEH612JPA--CGND-HRA-00543--Female--ALS_AD--Cortex_Frontal--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEH612JPA--CGND-HRA-00544--Female--ALS_AD--Cortex_Occipital--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEH612JPA--CGND-HRA-00544--Female--ALS_AD--Cortex_Occipital--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEH612JPA--CGND-HRA-00545--Female--ALS_AD--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEH612JPA--CGND-HRA-00545--Female--ALS_AD--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURX991BWB--CGND-HRA-00546--Female--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg_DCTN1_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURX991BWB--CGND-HRA-00546--Female--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg_DCTN1_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURX991BWB--CGND-HRA-00547--Female--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg_DCTN1_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURX991BWB--CGND-HRA-00547--Female--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg_DCTN1_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMK638LUX--CGND-HRA-00549--Male--ALS--Cerebellum--C9orf72_pos_SOD1_neg_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMK638LUX--CGND-HRA-00549--Male--ALS--Cerebellum--C9orf72_pos_SOD1_neg_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMK638LUX--CGND-HRA-00550--Male--ALS--Cortex_Frontal--C9orf72_pos_SOD1_neg_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMK638LUX--CGND-HRA-00550--Male--ALS--Cortex_Frontal--C9orf72_pos_SOD1_neg_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMK638LUX--CGND-HRA-00551--Male--ALS--Cortex_Occipital--C9orf72_pos_SOD1_neg_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMK638LUX--CGND-HRA-00551--Male--ALS--Cortex_Occipital--C9orf72_pos_SOD1_neg_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU73--CGND-HRA-00555--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg_NEFH_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU73--CGND-HRA-00555--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg_NEFH_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU73--CGND-HRA-00556--Female--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg_NEFH_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU73--CGND-HRA-00556--Female--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg_NEFH_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU73--CGND-HRA-00557--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg_NEFH_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU73--CGND-HRA-00557--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg_NEFH_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU73--CGND-HRA-00558--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg_NEFH_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU73--CGND-HRA-00558--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg_NEFH_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU74--CGND-HRA-00561--Male--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_pos_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU74--CGND-HRA-00561--Male--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_pos_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU74--CGND-HRA-00562--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_pos_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU74--CGND-HRA-00562--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_pos_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU82--CGND-HRA-00571--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU82--CGND-HRA-00571--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU82--CGND-HRA-00572--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU82--CGND-HRA-00572--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU82--CGND-HRA-00573--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU82--CGND-HRA-00573--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU82--CGND-HRA-00574--Male--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU82--CGND-HRA-00574--Male--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU82--CGND-HRA-00575--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU82--CGND-HRA-00575--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU82--CGND-HRA-00576--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU82--CGND-HRA-00576--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU82--CGND-HRA-00577--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU82--CGND-HRA-00577--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU83--CGND-HRA-00578--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU83--CGND-HRA-00578--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU83--CGND-HRA-00579--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU83--CGND-HRA-00579--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU83--CGND-HRA-00580--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU83--CGND-HRA-00580--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU83--CGND-HRA-00581--Male--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU83--CGND-HRA-00581--Male--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU83--CGND-HRA-00582--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU83--CGND-HRA-00582--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU83--CGND-HRA-00583--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU83--CGND-HRA-00583--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU83--CGND-HRA-00584--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU83--CGND-HRA-00584--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_pos_N139K_SPG11_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGY575NUQ--CGND-HRA-00585--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGY575NUQ--CGND-HRA-00585--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHA141EEC--CGND-HRA-00590--Male--Non-Neurological_Control--Cortex_Motor_Unspecified--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHA141EEC--CGND-HRA-00590--Male--Non-Neurological_Control--Cortex_Motor_Unspecified--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDA151YMK--CGND-HRA-00593--Female--Non-Neurological_Control--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDA151YMK--CGND-HRA-00593--Female--Non-Neurological_Control--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJB238MJR--CGND-HRA-00596--Male--Non-Neurological_Control--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJB238MJR--CGND-HRA-00596--Male--Non-Neurological_Control--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZB953VCD--CGND-HRA-00598--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZB953VCD--CGND-HRA-00598--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZB953VCD--CGND-HRA-00601--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZB953VCD--CGND-HRA-00601--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU75--CGND-HRA-00631--Female--ALS--Cortex_Motor_Unspecified--C9orf72_pos_SOD1_neg_OPTN_pos_SPG11_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU75--CGND-HRA-00631--Female--ALS--Cortex_Motor_Unspecified--C9orf72_pos_SOD1_neg_OPTN_pos_SPG11_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU77--CGND-HRA-00633--Male--ALS--Cortex_Motor_Unspecified--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU77--CGND-HRA-00633--Male--ALS--Cortex_Motor_Unspecified--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU77--CGND-HRA-00634--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU77--CGND-HRA-00634--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYY221HZA--CGND-HRA-00240--Male--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYY221HZA--CGND-HRA-00240--Male--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUCV649UJK--CGND-HRA-00243--Male--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUCV649UJK--CGND-HRA-00243--Male--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNL548ZBN--CGND-HRA-00244--Male--ALS_FTD--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNL548ZBN--CGND-HRA-00244--Male--ALS_FTD--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYY221HZA--CGND-HRA-00249--Male--ALS--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYY221HZA--CGND-HRA-00249--Male--ALS--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDW867LF9--CGND-HRA-00271--Male--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDW867LF9--CGND-HRA-00271--Male--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUE532LFF--CGND-HRA-00273--Male--ALS--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUE532LFF--CGND-HRA-00273--Male--ALS--Spinal_Cord_Lumbar--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURX991BWB--CGND-HRA-00548--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg_DCTN1_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURX991BWB--CGND-HRA-00548--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg_DCTN1_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMK638LUX--CGND-HRA-00552--Male--ALS--Spinal_Cord_Thoracic--C9orf72_pos_SOD1_neg_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMK638LUX--CGND-HRA-00552--Male--ALS--Spinal_Cord_Thoracic--C9orf72_pos_SOD1_neg_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGY575NUQ--CGND-HRA-00586--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGY575NUQ--CGND-HRA-00586--Male--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGY575NUQ--CGND-HRA-00587--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGY575NUQ--CGND-HRA-00587--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGY575NUQ--CGND-HRA-00588--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGY575NUQ--CGND-HRA-00588--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGY575NUQ--CGND-HRA-00589--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGY575NUQ--CGND-HRA-00589--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHA141EEC--CGND-HRA-00592--Male--Non-Neurological_Control--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHA141EEC--CGND-HRA-00592--Male--Non-Neurological_Control--Spinal_Cord_Lumbar--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDA151YMK--CGND-HRA-00594--Female--Non-Neurological_Control--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDA151YMK--CGND-HRA-00594--Female--Non-Neurological_Control--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDA151YMK--CGND-HRA-00595--Female--Non-Neurological_Control--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDA151YMK--CGND-HRA-00595--Female--Non-Neurological_Control--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZB953VCD--CGND-HRA-00599--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZB953VCD--CGND-HRA-00599--Female--ALS--Cortex_Motor_Medial--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZB953VCD--CGND-HRA-00600--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZB953VCD--CGND-HRA-00600--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAP156PM4--CGND-HRA-00603--Female--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAP156PM4--CGND-HRA-00603--Female--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAP156PM4--CGND-HRA-00604--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAP156PM4--CGND-HRA-00604--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAP156PM4--CGND-HRA-00605--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAP156PM4--CGND-HRA-00605--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAP156PM4--CGND-HRA-00606--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAP156PM4--CGND-HRA-00606--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUW911LWA--CGND-HRA-00609--Male--ALS_FTD--Spinal_Cord_Cervical--C9orf72_pos_SOD1_neg_NEFH_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUW911LWA--CGND-HRA-00609--Male--ALS_FTD--Spinal_Cord_Cervical--C9orf72_pos_SOD1_neg_NEFH_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNL974RU6--CGND-HRA-00620--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNL974RU6--CGND-HRA-00620--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNL974RU6--CGND-HRA-00621--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNL974RU6--CGND-HRA-00621--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNL974RU6--CGND-HRA-00622--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNL974RU6--CGND-HRA-00622--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNL974RU6--CGND-HRA-00623--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNL974RU6--CGND-HRA-00623--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGJ583BEE--CGND-HRA-01185--Male--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGJ583BEE--CGND-HRA-01185--Male--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGJ583BEE--CGND-HRA-01186--Male--Non-Neurological_Control--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGJ583BEE--CGND-HRA-01186--Male--Non-Neurological_Control--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGJ583BEE--CGND-HRA-01187--Male--Non-Neurological_Control--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGJ583BEE--CGND-HRA-01187--Male--Non-Neurological_Control--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEP010ZFE--CGND-HRA-01204--Male--Non-Neurological_Control--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEP010ZFE--CGND-HRA-01204--Male--Non-Neurological_Control--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEP010ZFE--CGND-HRA-01205--Male--Non-Neurological_Control--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEP010ZFE--CGND-HRA-01205--Male--Non-Neurological_Control--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUFE255AG2--CGND-HRA-01206--Male--ALS--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUFE255AG2--CGND-HRA-01206--Male--ALS--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUFE255AG2--CGND-HRA-01207--Male--ALS--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUFE255AG2--CGND-HRA-01207--Male--ALS--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUFF179PPT--CGND-HRA-01208--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUFF179PPT--CGND-HRA-01208--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUFF179PPT--CGND-HRA-01209--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUFF179PPT--CGND-HRA-01209--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZV622ZHF--CGND-HRA-01219--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg_SBMA_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZV622ZHF--CGND-HRA-01219--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg_SBMA_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZV622ZHF--CGND-HRA-01220--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg_SBMA_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZV622ZHF--CGND-HRA-01220--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg_SBMA_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWG523WRV--CGND-HRA-01222--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg_SETX_pos_CCNF_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWG523WRV--CGND-HRA-01222--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg_SETX_pos_CCNF_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWG523WRV--CGND-HRA-01223--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg_SETX_pos_CCNF_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWG523WRV--CGND-HRA-01223--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg_SETX_pos_CCNF_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWG523WRV--CGND-HRA-01224--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg_SETX_pos_CCNF_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWG523WRV--CGND-HRA-01224--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg_SETX_pos_CCNF_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHX090PGV--CGND-HRA-01225--Male--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHX090PGV--CGND-HRA-01225--Male--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHX090PGV--CGND-HRA-01227--Male--Non-Neurological_Control--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHX090PGV--CGND-HRA-01227--Male--Non-Neurological_Control--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUT049NND--CGND-HRA-01228--Female--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUT049NND--CGND-HRA-01228--Female--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTP414KZ2--CGND-HRA-01234--Female--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTP414KZ2--CGND-HRA-01234--Female--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTP414KZ2--CGND-HRA-01235--Female--Non-Neurological_Control--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTP414KZ2--CGND-HRA-01235--Female--Non-Neurological_Control--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUML172BXK--CGND-HRA-01236--Female--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUML172BXK--CGND-HRA-01236--Female--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXT258BD4--CGND-HRA-00239--Female--ALS--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXT258BD4--CGND-HRA-00239--Female--ALS--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUW911LWA--CGND-HRA-00539--Male--ALS_FTD--Cortex_Frontal--C9orf72_pos_SOD1_neg_NEFH_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUW911LWA--CGND-HRA-00539--Male--ALS_FTD--Cortex_Frontal--C9orf72_pos_SOD1_neg_NEFH_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUW911LWA--CGND-HRA-00607--Male--ALS_FTD--Cortex_Motor_Medial--C9orf72_pos_SOD1_neg_NEFH_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUW911LWA--CGND-HRA-00607--Male--ALS_FTD--Cortex_Motor_Medial--C9orf72_pos_SOD1_neg_NEFH_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUW911LWA--CGND-HRA-00608--Male--ALS_FTD--Cortex_Motor_Lateral--C9orf72_pos_SOD1_neg_NEFH_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUW911LWA--CGND-HRA-00608--Male--ALS_FTD--Cortex_Motor_Lateral--C9orf72_pos_SOD1_neg_NEFH_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUW911LWA--CGND-HRA-00610--Male--ALS_FTD--Spinal_Cord_Lumbar--C9orf72_pos_SOD1_neg_NEFH_pos_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUW911LWA--CGND-HRA-00610--Male--ALS_FTD--Spinal_Cord_Lumbar--C9orf72_pos_SOD1_neg_NEFH_pos_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEH612JPA--CGND-HRA-00611--Female--ALS_AD--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEH612JPA--CGND-HRA-00611--Female--ALS_AD--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEH612JPA--CGND-HRA-00613--Female--ALS_AD--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEH612JPA--CGND-HRA-00613--Female--ALS_AD--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEH612JPA--CGND-HRA-00614--Female--ALS_AD--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEH612JPA--CGND-HRA-00614--Female--ALS_AD--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURX991BWB--CGND-HRA-00615--Female--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg_DCTN1_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURX991BWB--CGND-HRA-00615--Female--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg_DCTN1_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURX991BWB--CGND-HRA-00616--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg_DCTN1_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURX991BWB--CGND-HRA-00616--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg_DCTN1_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUK557CZW--CGND-HRA-01212--Female--ALS_AD--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUK557CZW--CGND-HRA-01212--Female--ALS_AD--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUK557CZW--CGND-HRA-01213--Female--ALS_AD--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUK557CZW--CGND-HRA-01213--Female--ALS_AD--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-JHU74--CGND-HRA-01217--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_pos_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa JHU74--CGND-HRA-01217--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_pos_ANXA11_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKX037NKA--CGND-HRA-01218--Male--ALS_AD_FTD--Cortex_Frontal--C9orf72_pos_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKX037NKA--CGND-HRA-01218--Male--ALS_AD_FTD--Cortex_Frontal--C9orf72_pos_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUVB305VU7--CGND-HRA-01231--Male--ALS_AD_CTE--Cortex_Frontal--SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUVB305VU7--CGND-HRA-01231--Male--ALS_AD_CTE--Cortex_Frontal--SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUVB305VU7--CGND-HRA-01232--Male--ALS_AD_CTE--Cortex_Occipital--SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUVB305VU7--CGND-HRA-01232--Male--ALS_AD_CTE--Cortex_Occipital--SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUVB305VU7--CGND-HRA-01233--Male--ALS_AD_CTE--Spinal_Cord_Thoracic--SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUVB305VU7--CGND-HRA-01233--Male--ALS_AD_CTE--Spinal_Cord_Thoracic--SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUML172BXK--CGND-HRA-01237--Female--Non-Neurological_Control--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUML172BXK--CGND-HRA-01237--Female--Non-Neurological_Control--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUML172BXK--CGND-HRA-01238--Female--Non-Neurological_Control--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUML172BXK--CGND-HRA-01238--Female--Non-Neurological_Control--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXY076JMB--CGND-HRA-01239--Female--ALS--Cortex_Frontal--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXY076JMB--CGND-HRA-01239--Female--ALS--Cortex_Frontal--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXY076JMB--CGND-HRA-01240--Female--ALS--Cortex_Occipital--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXY076JMB--CGND-HRA-01240--Female--ALS--Cortex_Occipital--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXY076JMB--CGND-HRA-01241--Female--ALS--Spinal_Cord_Thoracic--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXY076JMB--CGND-HRA-01241--Female--ALS--Spinal_Cord_Thoracic--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEG442LDR--CGND-HRA-01242--Male--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEG442LDR--CGND-HRA-01242--Male--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEG442LDR--CGND-HRA-01243--Male--Non-Neurological_Control--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEG442LDR--CGND-HRA-01243--Male--Non-Neurological_Control--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEG442LDR--CGND-HRA-01244--Male--Non-Neurological_Control--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEG442LDR--CGND-HRA-01244--Male--Non-Neurological_Control--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEA633EN5--CGND-HRA-01245--Female--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEA633EN5--CGND-HRA-01245--Female--ALS--Cortex_Frontal--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEA633EN5--CGND-HRA-01246--Female--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEA633EN5--CGND-HRA-01246--Female--ALS--Cortex_Occipital--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEA633EN5--CGND-HRA-01247--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEA633EN5--CGND-HRA-01247--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWL993GU2--CGND-HRA-01248--Male--ALS--Cortex_Frontal--SOD1_neg_SETX_likely_benign_FIG4_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWL993GU2--CGND-HRA-01248--Male--ALS--Cortex_Frontal--SOD1_neg_SETX_likely_benign_FIG4_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZK186ZK4--CGND-HRA-01251--Female--ALS--Cortex_Frontal--SOD1_neg_UBQLN2_pos_SPG11_NEK1_ANG.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZK186ZK4--CGND-HRA-01251--Female--ALS--Cortex_Frontal--SOD1_neg_UBQLN2_pos_SPG11_NEK1_ANG.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZK186ZK4--CGND-HRA-01253--Female--ALS--Spinal_Cord_Thoracic--SOD1_neg_UBQLN2_pos_SPG11_NEK1_ANG.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZK186ZK4--CGND-HRA-01253--Female--ALS--Spinal_Cord_Thoracic--SOD1_neg_UBQLN2_pos_SPG11_NEK1_ANG.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGY575NUQ--CGND-HRA-01254--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGY575NUQ--CGND-HRA-01254--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGY575NUQ--CGND-HRA-01255--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGY575NUQ--CGND-HRA-01255--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGY575NUQ--CGND-HRA-01256--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGY575NUQ--CGND-HRA-01256--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHA141EEC--CGND-HRA-01257--Male--Non-Neurological_Control--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHA141EEC--CGND-HRA-01257--Male--Non-Neurological_Control--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDA151YMK--CGND-HRA-01258--Female--Non-Neurological_Control--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDA151YMK--CGND-HRA-01258--Female--Non-Neurological_Control--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDA151YMK--CGND-HRA-01259--Female--Non-Neurological_Control--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDA151YMK--CGND-HRA-01259--Female--Non-Neurological_Control--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJB238MJR--CGND-HRA-01260--Male--Non-Neurological_Control--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJB238MJR--CGND-HRA-01260--Male--Non-Neurological_Control--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJB238MJR--CGND-HRA-01261--Male--Non-Neurological_Control--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJB238MJR--CGND-HRA-01261--Male--Non-Neurological_Control--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZB953VCD--CGND-HRA-01263--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZB953VCD--CGND-HRA-01263--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZB953VCD--CGND-HRA-01264--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZB953VCD--CGND-HRA-01264--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZB953VCD--CGND-HRA-01265--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZB953VCD--CGND-HRA-01265--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEULN488RD5--CGND-HRA-01266--Male--ALS--Cortex_Frontal--C9orf72_neg_ATXN2_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEULN488RD5--CGND-HRA-01266--Male--ALS--Cortex_Frontal--C9orf72_neg_ATXN2_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEULN488RD5--CGND-HRA-01267--Male--ALS--Cortex_Occipital--C9orf72_neg_ATXN2_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEULN488RD5--CGND-HRA-01267--Male--ALS--Cortex_Occipital--C9orf72_neg_ATXN2_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAY067UTB--CGND-HRA-01269--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAY067UTB--CGND-HRA-01269--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURX991BWB--CGND-HRA-00618--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg_DCTN1_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURX991BWB--CGND-HRA-00618--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg_DCTN1_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAY067UTB--CGND-HRA-01270--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAY067UTB--CGND-HRA-01270--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKY135CV6--CGND-HRA-01283--Male--ALS_AD--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKY135CV6--CGND-HRA-01283--Male--ALS_AD--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKY135CV6--CGND-HRA-01284--Male--ALS_AD--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKY135CV6--CGND-HRA-01284--Male--ALS_AD--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYX020CB0--CGND-HRA-01285--Male--ALS_AD--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYX020CB0--CGND-HRA-01285--Male--ALS_AD--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEE593VY7--CGND-HRA-01291--Male--MSA--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEE593VY7--CGND-HRA-01291--Male--MSA--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEE593VY7--CGND-HRA-01292--Male--MSA--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEE593VY7--CGND-HRA-01292--Male--MSA--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMV641VYK--CGND-HRA-01293--Male--AD--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMV641VYK--CGND-HRA-01293--Male--AD--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMV641VYK--CGND-HRA-01294--Male--AD--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMV641VYK--CGND-HRA-01294--Male--AD--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDT233ZZ1--CGND-HRA-01297--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDT233ZZ1--CGND-HRA-01297--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDT233ZZ1--CGND-HRA-01298--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDT233ZZ1--CGND-HRA-01298--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG727NTW--CGND-HRA-01299--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG727NTW--CGND-HRA-01299--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG727NTW--CGND-HRA-01300--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG727NTW--CGND-HRA-01300--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEL133AK6--CGND-HRA-01327--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEL133AK6--CGND-HRA-01327--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEL133AK6--CGND-HRA-01328--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEL133AK6--CGND-HRA-01328--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYV496XLP--CGND-HRA-01329--Male--ALS_FTD_TM--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYV496XLP--CGND-HRA-01329--Male--ALS_FTD_TM--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZU200WEQ--CGND-HRA-01331--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZU200WEQ--CGND-HRA-01331--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUME287RK2--CGND-HRA-01333--Female--ALS_FTD--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUME287RK2--CGND-HRA-01333--Female--ALS_FTD--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEC006FND--CGND-HRA-01335--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEC006FND--CGND-HRA-01335--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKM699KKH--CGND-HRA-01337--Female--ALS_FTD--Cortex_Occipital--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKM699KKH--CGND-HRA-01337--Female--ALS_FTD--Cortex_Occipital--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWX086DGZ--CGND-HRA-01339--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWX086DGZ--CGND-HRA-01339--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJZ255ZC5--CGND-HRA-01341--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJZ255ZC5--CGND-HRA-01341--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHC282LVJ--CGND-HRA-01342--Female--Non-Neurological_Control--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHC282LVJ--CGND-HRA-01342--Female--Non-Neurological_Control--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHC282LVJ--CGND-HRA-01343--Female--Non-Neurological_Control--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHC282LVJ--CGND-HRA-01343--Female--Non-Neurological_Control--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXT979EZV--CGND-HRA-01344--Male--ALS_LB_FTD--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXT979EZV--CGND-HRA-01344--Male--ALS_LB_FTD--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXT979EZV--CGND-HRA-01345--Male--ALS_LB_FTD--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXT979EZV--CGND-HRA-01345--Male--ALS_LB_FTD--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJL308UBK--CGND-HRA-01349--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJL308UBK--CGND-HRA-01349--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMY028JH4--CGND-HRA-01352--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMY028JH4--CGND-HRA-01352--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMY028JH4--CGND-HRA-01353--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMY028JH4--CGND-HRA-01353--Female--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMY028JH4--CGND-HRA-01354--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMY028JH4--CGND-HRA-01354--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMY028JH4--CGND-HRA-01355--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMY028JH4--CGND-HRA-01355--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEF856BLV--CGND-HRA-00460--Female--ALS--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEF856BLV--CGND-HRA-00460--Female--ALS--Cortex_Frontal--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEF856BLV--CGND-HRA-00465--Female--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEF856BLV--CGND-HRA-00465--Female--ALS--Cerebellum--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUCG551GV1--CGND-HRA-00466--Female--Peripheral_Neuropathy--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUCG551GV1--CGND-HRA-00466--Female--Peripheral_Neuropathy--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUCG551GV1--CGND-HRA-00469--Female--Peripheral_Neuropathy--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUCG551GV1--CGND-HRA-00469--Female--Peripheral_Neuropathy--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGY741GH8--CGND-HRA-00476--Male--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGY741GH8--CGND-HRA-00476--Male--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGY741GH8--CGND-HRA-00479--Male--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGY741GH8--CGND-HRA-00479--Male--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGY741GH8--CGND-HRA-00480--Male--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGY741GH8--CGND-HRA-00480--Male--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUFE255AG2--CGND-HRA-00481--Male--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUFE255AG2--CGND-HRA-00481--Male--ALS--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUFE255AG2--CGND-HRA-00486--Male--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUFE255AG2--CGND-HRA-00486--Male--ALS--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUFF179PPT--CGND-HRA-00487--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUFF179PPT--CGND-HRA-00487--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUFF179PPT--CGND-HRA-00492--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUFF179PPT--CGND-HRA-00492--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZV622ZHF--CGND-HRA-00636--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg_SBMA_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZV622ZHF--CGND-HRA-00636--Male--ALS--Cerebellum--C9orf72_neg_SOD1_neg_SBMA_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXY076JMB--CGND-HRA-00662--Female--ALS--Cerebellum--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXY076JMB--CGND-HRA-00662--Female--ALS--Cerebellum--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEA633EN5--CGND-HRA-00671--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEA633EN5--CGND-HRA-00671--Female--ALS--Cerebellum--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEA633EN5--CGND-HRA-00672--Female--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEA633EN5--CGND-HRA-00672--Female--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAY067UTB--CGND-HRA-00746--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAY067UTB--CGND-HRA-00746--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEP010ZFE--CGND-HRA-01179--Male--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEP010ZFE--CGND-HRA-01179--Male--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEULN488RD5--CGND-HRA-01268-2--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_ATXN2_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEULN488RD5--CGND-HRA-01268-2--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_ATXN2_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYX020CB0--CGND-HRA-01286--Male--ALS_AD--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYX020CB0--CGND-HRA-01286--Male--ALS_AD--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMT947ALA--CGND-HRA-01287--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMT947ALA--CGND-HRA-01287--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNE940RZC--CGND-HRA-01289--Male--AD--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNE940RZC--CGND-HRA-01289--Male--AD--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWP285RM6--CGND-HRA-01295--Female--ALS_AD--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWP285RM6--CGND-HRA-01295--Female--ALS_AD--Cortex_Occipital--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWP285RM6--CGND-HRA-01296--Female--ALS_AD--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWP285RM6--CGND-HRA-01296--Female--ALS_AD--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTB398FC9--CGND-HRA-01302--Male--ALS--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTB398FC9--CGND-HRA-01302--Male--ALS--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUYV496XLP--CGND-HRA-01330--Male--ALS_FTD_TM--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUYV496XLP--CGND-HRA-01330--Male--ALS_FTD_TM--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZU200WEQ--CGND-HRA-01332--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZU200WEQ--CGND-HRA-01332--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKM699KKH--CGND-HRA-01336--Female--ALS_FTD--Spinal_Cord_Thoracic--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKM699KKH--CGND-HRA-01336--Female--ALS_FTD--Spinal_Cord_Thoracic--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWX086DGZ--CGND-HRA-01338--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWX086DGZ--CGND-HRA-01338--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJZ255ZC5--CGND-HRA-01340--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJZ255ZC5--CGND-HRA-01340--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJL308UBK--CGND-HRA-01348--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJL308UBK--CGND-HRA-01348--Female--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUJL308UBK--CGND-HRA-01350--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUJL308UBK--CGND-HRA-01350--Female--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXR145UBL--CGND-HRA-01356--Male--ALS_FTD--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXR145UBL--CGND-HRA-01356--Male--ALS_FTD--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXR145UBL--CGND-HRA-01357--Male--ALS_FTD--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXR145UBL--CGND-HRA-01357--Male--ALS_FTD--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXR145UBL--CGND-HRA-01358--Male--ALS_FTD--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXR145UBL--CGND-HRA-01358--Male--ALS_FTD--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXR145UBL--CGND-HRA-01359--Male--ALS_FTD--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXR145UBL--CGND-HRA-01359--Male--ALS_FTD--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKN209FNW--CGND-HRA-01360--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_pos_AV4.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKN209FNW--CGND-HRA-01360--Male--ALS--Cortex_Occipital--C9orf72_neg_SOD1_pos_AV4.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKN209FNW--CGND-HRA-01361--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_pos_AV4.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKN209FNW--CGND-HRA-01361--Male--ALS--Cortex_Frontal--C9orf72_neg_SOD1_pos_AV4.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKN209FNW--CGND-HRA-01362--Male--ALS--Cerebellum--C9orf72_neg_SOD1_pos_AV4.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKN209FNW--CGND-HRA-01362--Male--ALS--Cerebellum--C9orf72_neg_SOD1_pos_AV4.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUKN209FNW--CGND-HRA-01363--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_pos_AV4.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUKN209FNW--CGND-HRA-01363--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_pos_AV4.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUF289NRL--CGND-HRA-01364--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUF289NRL--CGND-HRA-01364--Male--ALS--Cortex_Occipital--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUF289NRL--CGND-HRA-01365--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUF289NRL--CGND-HRA-01365--Male--ALS--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUF289NRL--CGND-HRA-01366--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUF289NRL--CGND-HRA-01366--Male--ALS--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUF289NRL--CGND-HRA-01367--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUF289NRL--CGND-HRA-01367--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUPU334DL1--CGND-HRA-01369--Female--ALS_FTD--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUPU334DL1--CGND-HRA-01369--Female--ALS_FTD--Cortex_Frontal--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUPU334DL1--CGND-HRA-01370--Female--ALS_FTD--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUPU334DL1--CGND-HRA-01370--Female--ALS_FTD--Cerebellum--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGV399KJW--CGND-HRA-00371--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGV399KJW--CGND-HRA-00371--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHX090PGV--CGND-HRA-00643--Male--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHX090PGV--CGND-HRA-00643--Male--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWL993GU2--CGND-HRA-00676--Male--ALS--Cerebellum--SOD1_neg_SETX_likely_benign_FIG4_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWL993GU2--CGND-HRA-00676--Male--ALS--Cerebellum--SOD1_neg_SETX_likely_benign_FIG4_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEULN488RD5--CGND-HRA-00731--Male--ALS--Cerebellum--C9orf72_neg_ATXN2_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEULN488RD5--CGND-HRA-00731--Male--ALS--Cerebellum--C9orf72_neg_ATXN2_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEP010ZFE--CGND-HRA-01178--Male--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEP010ZFE--CGND-HRA-01178--Male--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUPU334DL1--CGND-HRA-01371--Female--ALS_FTD--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUPU334DL1--CGND-HRA-01371--Female--ALS_FTD--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWC334RTZ--CGND-HRA-01372--Male--ALS_CTE--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWC334RTZ--CGND-HRA-01372--Male--ALS_CTE--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWC334RTZ--CGND-HRA-01373--Male--ALS_CTE--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWC334RTZ--CGND-HRA-01373--Male--ALS_CTE--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWD570BTK--CGND-HRA-01378--Male--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWD570BTK--CGND-HRA-01378--Male--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWD570BTK--CGND-HRA-01379--Male--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWD570BTK--CGND-HRA-01379--Male--Non-Neurological_Control--Cortex_Frontal--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTL441LZ7--CGND-HRA-00322--Male--ALS--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTL441LZ7--CGND-HRA-00322--Male--ALS--Spinal_Cord_Cervical--C9orf72_pos.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUDG727NTW--CGND-HRA-00431-2--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUDG727NTW--CGND-HRA-00431-2--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUAP156PM4--CGND-HRA-00537--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUAP156PM4--CGND-HRA-00537--Female--ALS--Spinal_Cord_Thoracic--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURX991BWB--CGND-HRA-00617-2--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg_DCTN1_pos_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURX991BWB--CGND-HRA-00617-2--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg_DCTN1_pos_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNL974RU6--CGND-HRA-00624--Male--ALS--Cortex_Motor_Unspecified--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNL974RU6--CGND-HRA-00624--Male--ALS--Cortex_Motor_Unspecified--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNL974RU6--CGND-HRA-00625--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNL974RU6--CGND-HRA-00625--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNL974RU6--CGND-HRA-00626--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNL974RU6--CGND-HRA-00626--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZV622ZHF--CGND-HRA-00637--Male--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg_SBMA_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZV622ZHF--CGND-HRA-00637--Male--ALS--Cortex_Motor_Medial--C9orf72_neg_SOD1_neg_SBMA_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZV622ZHF--CGND-HRA-00638--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg_SBMA_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZV622ZHF--CGND-HRA-00638--Male--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg_SBMA_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWG523WRV--CGND-HRA-00640--Male--ALS--Cortex_Motor_Unspecified--C9orf72_neg_SOD1_neg_SETX_pos_CCNF_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWG523WRV--CGND-HRA-00640--Male--ALS--Cortex_Motor_Unspecified--C9orf72_neg_SOD1_neg_SETX_pos_CCNF_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWG523WRV--CGND-HRA-00641--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg_SETX_pos_CCNF_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWG523WRV--CGND-HRA-00641--Male--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg_SETX_pos_CCNF_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWG523WRV--CGND-HRA-00642--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg_SETX_pos_CCNF_likely_benign.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWG523WRV--CGND-HRA-00642--Male--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg_SETX_pos_CCNF_likely_benign.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHX090PGV--CGND-HRA-00644--Male--Non-Neurological_Control--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHX090PGV--CGND-HRA-00644--Male--Non-Neurological_Control--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUHX090PGV--CGND-HRA-00645--Male--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUHX090PGV--CGND-HRA-00645--Male--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURJ387PPV--CGND-HRA-00648--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURJ387PPV--CGND-HRA-00648--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEURJ387PPV--CGND-HRA-00649--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEURJ387PPV--CGND-HRA-00649--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUVB305VU7--CGND-HRA-00650--Male--ALS_AD_CTE--Cortex_Motor_Medial--SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUVB305VU7--CGND-HRA-00650--Male--ALS_AD_CTE--Cortex_Motor_Medial--SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUVB305VU7--CGND-HRA-00651--Male--ALS_AD_CTE--Cortex_Motor_Lateral--SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUVB305VU7--CGND-HRA-00651--Male--ALS_AD_CTE--Cortex_Motor_Lateral--SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUVB305VU7--CGND-HRA-00652--Male--ALS_AD_CTE--Spinal_Cord_Cervical--SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUVB305VU7--CGND-HRA-00652--Male--ALS_AD_CTE--Spinal_Cord_Cervical--SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTP414KZ2--CGND-HRA-00658--Female--Non-Neurological_Control--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTP414KZ2--CGND-HRA-00658--Female--Non-Neurological_Control--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUTP414KZ2--CGND-HRA-00659--Female--Non-Neurological_Control--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUTP414KZ2--CGND-HRA-00659--Female--Non-Neurological_Control--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUML172BXK--CGND-HRA-00660--Female--Non-Neurological_Control--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUML172BXK--CGND-HRA-00660--Female--Non-Neurological_Control--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUML172BXK--CGND-HRA-00661--Female--Non-Neurological_Control--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUML172BXK--CGND-HRA-00661--Female--Non-Neurological_Control--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXY076JMB--CGND-HRA-00663--Female--ALS--Cortex_Motor_Medial--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXY076JMB--CGND-HRA-00663--Female--ALS--Cortex_Motor_Medial--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXY076JMB--CGND-HRA-00664--Female--ALS--Cortex_Motor_Lateral--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXY076JMB--CGND-HRA-00664--Female--ALS--Cortex_Motor_Lateral--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXY076JMB--CGND-HRA-00665--Female--ALS--Spinal_Cord_Cervical--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXY076JMB--CGND-HRA-00665--Female--ALS--Spinal_Cord_Cervical--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUXY076JMB--CGND-HRA-00666--Female--ALS--Spinal_Cord_Lumbar--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUXY076JMB--CGND-HRA-00666--Female--ALS--Spinal_Cord_Lumbar--SOD1_neg_FIG4_pos_SETX_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEG442LDR--CGND-HRA-00667--Male--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEG442LDR--CGND-HRA-00667--Male--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEG442LDR--CGND-HRA-00668--Male--Non-Neurological_Control--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEG442LDR--CGND-HRA-00668--Male--Non-Neurological_Control--Cortex_Motor_Medial--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEG442LDR--CGND-HRA-00669--Male--Non-Neurological_Control--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEG442LDR--CGND-HRA-00669--Male--Non-Neurological_Control--Cortex_Motor_Lateral--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEG442LDR--CGND-HRA-00670--Male--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEG442LDR--CGND-HRA-00670--Male--Non-Neurological_Control--Spinal_Cord_Cervical--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEA633EN5--CGND-HRA-00673--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEA633EN5--CGND-HRA-00673--Female--ALS--Cortex_Motor_Lateral--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEA633EN5--CGND-HRA-00674--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEA633EN5--CGND-HRA-00674--Female--ALS--Spinal_Cord_Cervical--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUEA633EN5--CGND-HRA-00675--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUEA633EN5--CGND-HRA-00675--Female--ALS--Spinal_Cord_Lumbar--C9orf72_neg_SOD1_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZK186ZK4--CGND-HRA-00680--Female--ALS--Cortex_Motor_Medial--SOD1_neg_UBQLN2_pos_SPG11_NEK1_ANG.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZK186ZK4--CGND-HRA-00680--Female--ALS--Cortex_Motor_Medial--SOD1_neg_UBQLN2_pos_SPG11_NEK1_ANG.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUZK186ZK4--CGND-HRA-00681--Female--ALS--Cortex_Motor_Lateral--SOD1_neg_UBQLN2_pos_SPG11_NEK1_ANG.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUZK186ZK4--CGND-HRA-00681--Female--ALS--Cortex_Motor_Lateral--SOD1_neg_UBQLN2_pos_SPG11_NEK1_ANG.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUGJ583BEE--CGND-HRA-01184-2--Male--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUGJ583BEE--CGND-HRA-01184-2--Male--Non-Neurological_Control--Cerebellum--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUUT049NND--CGND-HRA-01230--Female--Non-Neurological_Control--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUUT049NND--CGND-HRA-01230--Female--Non-Neurological_Control--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUWL993GU2--CGND-HRA-01250--Male--ALS--Spinal_Cord_Thoracic--SOD1_neg_SETX_likely_benign_FIG4_VUS.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUWL993GU2--CGND-HRA-01250--Male--ALS--Spinal_Cord_Thoracic--SOD1_neg_SETX_likely_benign_FIG4_VUS.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUMT947ALA--CGND-HRA-01288-2--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUMT947ALA--CGND-HRA-01288-2--Male--ALS--Spinal_Cord_Thoracic--C9orf72_neg.hg19-refSeq.2x50mers.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-NEUNE940RZC--CGND-HRA-01290-2--Male--AD--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/refMrna.withNames.fa NEUNE940RZC--CGND-HRA-01290-2--Male--AD--Spinal_Cord_Thoracic--Unknown.hg19-refSeq.2x50mers.a.e200.offrate1.bam