cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_elegans_E1-ASM64827v1.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1.fa - -o Holospora_elegans_E1-ASM64827v1.100mers.nuclear.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_elegans_E1-ASM64827v1.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1.fa - -o Holospora_elegans_E1-ASM64827v1.150mers.nuclear.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_elegans_E1-ASM64827v1.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1.fa - -o Holospora_elegans_E1-ASM64827v1.50mers.nuclear.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_obtusa_F1-ASM46966v2.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1.fa - -o Holospora_obtusa_F1-ASM46966v2.100mers.nuclear.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_obtusa_F1-ASM46966v2.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1.fa - -o Holospora_obtusa_F1-ASM46966v2.150mers.nuclear.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_obtusa_F1-ASM46966v2.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1.fa - -o Holospora_obtusa_F1-ASM46966v2.50mers.nuclear.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_undulata_HU1-ASM38817v3.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1.fa - -o Holospora_undulata_HU1-ASM38817v3.100mers.nuclear.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_undulata_HU1-ASM38817v3.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1.fa - -o Holospora_undulata_HU1-ASM38817v3.150mers.nuclear.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_undulata_HU1-ASM38817v3.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1.fa - -o Holospora_undulata_HU1-ASM38817v3.50mers.nuclear.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_elegans_E1-ASM64827v1.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o Holospora_elegans_E1-ASM64827v1.100mers.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_elegans_E1-ASM64827v1.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o Holospora_elegans_E1-ASM64827v1.150mers.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_elegans_E1-ASM64827v1.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o Holospora_elegans_E1-ASM64827v1.50mers.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_obtusa_F1-ASM46966v2.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o Holospora_obtusa_F1-ASM46966v2.100mers.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_obtusa_F1-ASM46966v2.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o Holospora_obtusa_F1-ASM46966v2.150mers.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_obtusa_F1-ASM46966v2.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o Holospora_obtusa_F1-ASM46966v2.50mers.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_undulata_HU1-ASM38817v3.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o Holospora_undulata_HU1-ASM38817v3.100mers.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_undulata_HU1-ASM38817v3.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o Holospora_undulata_HU1-ASM38817v3.150mers.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_undulata_HU1-ASM38817v3.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_annotation_v1.transcriptome.fa - -o Holospora_undulata_HU1-ASM38817v3.50mers.transcriptome.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_elegans_E1-ASM64827v1.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion.fa - -o Holospora_elegans_E1-ASM64827v1.100mers.mito.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_elegans_E1-ASM64827v1.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion.fa - -o Holospora_elegans_E1-ASM64827v1.150mers.mito.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_elegans_E1-ASM64827v1.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion.fa - -o Holospora_elegans_E1-ASM64827v1.50mers.mito.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_obtusa_F1-ASM46966v2.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion.fa - -o Holospora_obtusa_F1-ASM46966v2.100mers.mito.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_obtusa_F1-ASM46966v2.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion.fa - -o Holospora_obtusa_F1-ASM46966v2.150mers.mito.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_obtusa_F1-ASM46966v2.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion.fa - -o Holospora_obtusa_F1-ASM46966v2.50mers.mito.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_undulata_HU1-ASM38817v3.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion.fa - -o Holospora_undulata_HU1-ASM38817v3.100mers.mito.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_undulata_HU1-ASM38817v3.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion.fa - -o Holospora_undulata_HU1-ASM38817v3.150mers.mito.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Holospora_undulata_HU1-ASM38817v3.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/Paramecium_caudatum-mitochondrion.fa - -o Holospora_undulata_HU1-ASM38817v3.50mers.mito.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic.fa - -o Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.100mers.Holospora_elegans_E1-ASM64827v1.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic.fa - -o Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.150mers.Holospora_elegans_E1-ASM64827v1.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic.fa - -o Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.50mers.Holospora_elegans_E1-ASM64827v1.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.100mers.Holospora_elegans_E1-ASM64827v1.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.150mers.Holospora_elegans_E1-ASM64827v1.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.50mers.Holospora_elegans_E1-ASM64827v1.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.100mers.Holospora_elegans_E1-ASM64827v1.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.150mers.Holospora_elegans_E1-ASM64827v1.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_elegans_E1-ASM64827v1/bowtie-indexes/GCA_000648275.1_ASM64827v1_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.50mers.Holospora_elegans_E1-ASM64827v1.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic.fa - -o Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.100mers.Holospora_obtusa_F1-ASM46966v2.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic.fa - -o Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.150mers.Holospora_obtusa_F1-ASM46966v2.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic.fa - -o Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.50mers.Holospora_obtusa_F1-ASM46966v2.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.100mers.Holospora_obtusa_F1-ASM46966v2.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.150mers.Holospora_obtusa_F1-ASM46966v2.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.50mers.Holospora_obtusa_F1-ASM46966v2.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.100mers.Holospora_obtusa_F1-ASM46966v2.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.150mers.Holospora_obtusa_F1-ASM46966v2.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_obtusa_F1-ASM46966v2/bowtie-indexes/GCA_000469665.2_ASM46966v2_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.50mers.Holospora_obtusa_F1-ASM46966v2.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic.fa - -o Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.100mers.Holospora_undulata_HU1-ASM38817v3.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic.fa - -o Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.150mers.Holospora_undulata_HU1-ASM38817v3.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic.fa - -o Paramecium_caudatum_43c3d-Paramecium_caudatum-mitochondrion.50mers.Holospora_undulata_HU1-ASM38817v3.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.100mers.Holospora_undulata_HU1-ASM38817v3.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.150mers.Holospora_undulata_HU1-ASM38817v3.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_annotation_v1.transcriptome.50mers.Holospora_undulata_HU1-ASM38817v3.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.100mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.100mers.Holospora_undulata_HU1-ASM38817v3.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.150mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.150mers.Holospora_undulata_HU1-ASM38817v3.bam
cd /N/dc2/projects/marinovg/2015-05-22-Holospora-mappability; cat Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.50mers.fa | /N/dc2/projects/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic -p 16 -v 3 -a --offrate 1 -t -f --sam-nh --sam - | samtools view -bT /N/dc2/projects/marinovg/genomes/Bacteria/Holospora_undulata_HU1-ASM38817v3/bowtie-indexes/GCA_000388175.3_ASM38817v3_genomic.fa - -o Paramecium_caudatum_43c3d-caudatum_43c3d_assembly_v1.50mers.Holospora_undulata_HU1-ASM38817v3.bam