export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_decaurelia-223/pdecaurelia_223_annotation_v1.0.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_decaurelia-223/transcriptome-indexes/pdecaurelia_223_annotation_v1.0 -o Paramecium_decaurelia-223-GSF1240-DE1_S2-2x80-TopHat-2.0.8-minIntron10-genome+mito /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_decaurelia-223/bowtie-indexes/pdecaurelia_mac_223_v1.0+chrM /oak/stanford/groups/akundaje/marinovg/Paramecium/RNA-seq/reads/GSF1240/GSF1240-DE1_S2_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/Paramecium/RNA-seq/reads/GSF1240/GSF1240-DE1_S2_R2_001.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --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 /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_dodecaurelia-274/pdodecaurelia_274_annotation_v1.0.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_dodecaurelia-274/transcriptome-indexes/pdodecaurelia_274_annotation_v1.0 -o Paramecium_dodecaurelia-274-GSF1240-DO1_S1-2x80-TopHat-2.0.8-minIntron10-genome+mito /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_dodecaurelia-274/bowtie-indexes/pdodecaurelia_mac_274_v1.0+chrM /oak/stanford/groups/akundaje/marinovg/Paramecium/RNA-seq/reads/GSF1240/GSF1240-DO1_S1_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/Paramecium/RNA-seq/reads/GSF1240/GSF1240-DO1_S1_R2_001.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_jenningsi-M/pjenningsi_M_annotation_v1.0.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_jenningsi-M/transcriptome-indexes/pjenningsi_M_annotation_v1.0 -o Paramecium_jenningsi-M-GSF1240-J1_S6-2x80-TopHat-2.0.8-minIntron10-genome+mito /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_jenningsi-M/bowtie-indexes/pjenningsi_mac_M_v1.0+chrM /oak/stanford/groups/akundaje/marinovg/Paramecium/RNA-seq/reads/GSF1240/GSF1240-J1_S6_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/Paramecium/RNA-seq/reads/GSF1240/GSF1240-J1_S6_R2_001.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --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 /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_novaurelia-TE/pnovaurelia_TE_annotation_v1.0.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_novaurelia-TE/transcriptome-indexes/pnovaurelia_TE_annotation_v1.0 -o Paramecium_novaurelia-TE-GSF1240-N1_S5-2x80-TopHat-2.0.8-minIntron10-genome+mito /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_novaurelia-TE/bowtie-indexes/pnovaurelia_mac_TE_v1.0+chrM /oak/stanford/groups/akundaje/marinovg/Paramecium/RNA-seq/reads/GSF1240/GSF1240-N1_S5_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/Paramecium/RNA-seq/reads/GSF1240/GSF1240-N1_S5_R2_001.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --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 /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_quadecaurelia-N1A/pquadecaurelia_NiA_annotation_v1.0.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_quadecaurelia-N1A/transcriptome-indexes/pquadecaurelia_NiA_annotation_v1.0 -o Paramecium_quadecaurelia-N1A-GSF1240-DE1_S2-2x80-TopHat-2.0.8-minIntron10-genome+mito /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Paramecium_quadecaurelia-N1A/bowtie-indexes/pquadecaurelia_mac_NiA_v1.0+chrM /oak/stanford/groups/akundaje/marinovg/Paramecium/RNA-seq/reads/GSF1240/GSF1240-Q1_S4_R1_001.fastq.gz /oak/stanford/groups/akundaje/marinovg/Paramecium/RNA-seq/reads/GSF1240/GSF1240-Q1_S4_R2_001.fastq.gz