cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/transcriptome-indexes/biaurelia_V1-4_annotation_v1 -o Paramecium-biaurelia-Sample_2V-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 Sample_2V.end1.fastq.bz2 Sample_2V.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/transcriptome-indexes/biaurelia_V1-4_annotation_v1 -o Paramecium-biaurelia-Sample_bi-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 Sample_bi.end1.fastq.bz2 Sample_bi.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/transcriptome-indexes/biaurelia_V1-4_annotation_v1 -o Paramecium-biaurelia-Sample_2D1-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 Sample_2D1.end1.fastq.bz2 Sample_2D1.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/transcriptome-indexes/biaurelia_V1-4_annotation_v1 -o Paramecium-biaurelia-Sample_2D2-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 Sample_2D2.end1.fastq.bz2 Sample_2D2.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/transcriptome-indexes/caudatum_43c3d_annotation_v1 -o Paramecium-caudatum-strain_43c3d-Sample_c3d_1-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 Sample_c3d_1.end1.fastq.bz2 Sample_c3d_1.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/transcriptome-indexes/caudatum_43c3d_annotation_v1 -o Paramecium-caudatum-strain_43c3d-Sample_c3d_2-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 Sample_c3d_2.end1.fastq.bz2 Sample_c3d_2.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/transcriptome-indexes/caudatum_43c3d_annotation_v1 -o Paramecium-caudatum-strain_43c3d-Sample_MPF1-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 Sample_MPF1.end1.fastq.bz2 Sample_MPF1.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/transcriptome-indexes/primaurelia_Ir4-2_annotation_v1 -o Paramecium_primaurelia-Sample_1V-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1 Sample_1V.end1.fastq.bz2 Sample_1V.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/transcriptome-indexes/primaurelia_Ir4-2_annotation_v1 -o Paramecium_primaurelia-Sample_1D1-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1 Sample_1D1.end1.fastq.bz2 Sample_1D1.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/transcriptome-indexes/primaurelia_Ir4-2_annotation_v1 -o Paramecium_primaurelia-Sample_1D2-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1 Sample_1D2.end1.fastq.bz2 Sample_1D2.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/transcriptome-indexes/sexaurelia_AZ8-4_annotation_v1 -o Paramecium-sexaurelia-Sample_6D1-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1 Sample_6D1.end1.fastq.bz2 Sample_6D1.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/transcriptome-indexes/sexaurelia_AZ8-4_annotation_v1 -o Paramecium-sexaurelia-Sample_6D2-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1 Sample_6D2.end1.fastq.bz2 Sample_6D2.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/transcriptome-indexes/sexaurelia_AZ8-4_annotation_v1 -o Paramecium-sexaurelia-Sample_6V-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1 Sample_6V.end1.fastq.bz2 Sample_6V.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/transcriptome-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 -o Paramecium_tetraurelia-Sample_4D_2_14_16_12-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 Sample_4D_2_14_16_12.end1.fastq.bz2 Sample_4D_2_14_16_12.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/transcriptome-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 -o Paramecium_tetraurelia-Sample_4D1-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 Sample_4D1.end1.fastq.bz2 Sample_4D1.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/transcriptome-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 -o Paramecium_tetraurelia-Sample_4D2-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 Sample_4D2.end1.fastq.bz2 Sample_4D2.end2.fastq.bz2
cd /N/dc2/projects/marinovg/2015-02-24-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/transcriptome-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 -o Paramecium_tetraurelia-Sample_172-2x150-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 Sample_172.end1.fastq.bz2 Sample_172.end2.fastq.bz2