cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/transcriptome-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 -o Paramecium_tetraurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 GSF869-Doak-Ugne-209_S7_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-209_S7_R2_001.100mers.fastq.gz
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$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-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 GSF869-Doak-Ugne-223_S10_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-223_S10_R2_001.100mers.fastq.gz 
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/transcriptome-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 -o Paramecium_tetraurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 GSF869-Doak-Ugne-227_S13_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-227_S13_R2_001.100mers.fastq.gz 
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$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-GSF869-Doak-Ugne-328_S12-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 GSF869-Doak-Ugne-328_S12_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-328_S12_R2_001.100mers.fastq.gz 
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/Paramecium_tetraurelia.GCA_000165425.1.20.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/transcriptome-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 -o Paramecium_tetraurelia-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 GSF869-Doak-Ugne-NiA_S11_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-NiA_S11_R2_001.100mers.fastq.gz 
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$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-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 GSF869-Doak-Ugne-223_S10_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-223_S10_R2_001.100mers.fastq.gz 
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/transcriptome-indexes/biaurelia_V1-4_annotation_v1 -o Paramecium-biaurelia-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 GSF869-Doak-Ugne-NiA_S11_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-NiA_S11_R2_001.100mers.fastq.gz 
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$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-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 GSF869-Doak-Ugne-V1-4_S9_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-V1-4_S9_R2_001.100mers.fastq.gz 
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/transcriptome-indexes/primaurelia_Ir4-2_annotation_v1 -o Paramecium_primaurelia-GSF869-Doak-Ugne-223_S10-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1 GSF869-Doak-Ugne-223_S10_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-223_S10_R2_001.100mers.fastq.gz 
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$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-GSF869-Doak-Ugne-NiA_S11-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1 GSF869-Doak-Ugne-NiA_S11_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-NiA_S11_R2_001.100mers.fastq.gz 
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/transcriptome-indexes/primaurelia_Ir4-2_annotation_v1 -o Paramecium_primaurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1 GSF869-Doak-Ugne-227_S13_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-227_S13_R2_001.100mers.fastq.gz 
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$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-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/bowtie-indexes/primaurelia_Ir4-2_assembly_v1 GSF869-Doak-Ugne-V1-4_S9_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-V1-4_S9_R2_001.100mers.fastq.gz 
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/transcriptome-indexes/sexaurelia_AZ8-4_annotation_v1 -o Paramecium-sexaurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1 GSF869-Doak-Ugne-227_S13_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-227_S13_R2_001.100mers.fastq.gz 
cd /N/dc2/projects/marinovg/2015-06-12-Ugne-data; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$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-GSF869-Doak-Ugne-V1-4_S9-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1 GSF869-Doak-Ugne-V1-4_S9_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-V1-4_S9_R2_001.100mers.fastq.gz