cd /N/dc2/projects/marinovg/2015-02-13-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:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/transcriptome-indexes/biaurelia_V1-4_annotation_v1 -o /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq/Paramecium-biaurelia-strain_V1-4-autogamy-141105-bi-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 /N/dc2/projects/paramecium/RAW_DATA/Paramecium/biaurelia/strain_V1-4/RNA/autogamy/141105/bi_CCGTCCCG_L001_R1_001.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Paramecium/biaurelia/strain_V1-4/RNA/autogamy/141105/bi_CCGTCCCG_L001_R3_001.fastq.gz
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$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 /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq/Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 /N/dc2/projects/paramecium/RAW_DATA/Paramecium/biaurelia/strain_V1-4/RNA/vegetative/110506_IRIS_00020/para1_1_sequence.txt.gz /N/dc2/projects/paramecium/RAW_DATA/Paramecium/biaurelia/strain_V1-4/RNA/vegetative/110506_IRIS_00020/para1_2_sequence.txt.gz
cd /N/dc2/projects/marinovg/2015-02-13-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:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/transcriptome-indexes/biaurelia_V1-4_annotation_v1 -o /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq/Paramecium-biaurelia-strain_V1-4-vegetative-141105-2V-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/bowtie-indexes/biaurelia_V1-4_assembly_v1 /N/dc2/projects/paramecium/RAW_DATA/Paramecium/biaurelia/strain_V1-4/RNA/vegetative/141105/2V_AGTCAACA_L001_R1_001.fastq.gz,/N/dc2/projects/paramecium/RAW_DATA/Paramecium/biaurelia/strain_V1-4/RNA/vegetative/141105/2V_AGTCAACA_L001_R1_002.fastq.gz,/N/dc2/projects/paramecium/RAW_DATA/Paramecium/biaurelia/strain_V1-4/RNA/vegetative/141105/2V_AGTCAACA_L001_R1_003.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Paramecium/biaurelia/strain_V1-4/RNA/vegetative/141105/2V_AGTCAACA_L001_R3_001.fastq.gz,/N/dc2/projects/paramecium/RAW_DATA/Paramecium/biaurelia/strain_V1-4/RNA/vegetative/141105/2V_AGTCAACA_L001_R3_002.fastq.gz,/N/dc2/projects/paramecium/RAW_DATA/Paramecium/biaurelia/strain_V1-4/RNA/vegetative/141105/2V_AGTCAACA_L001_R3_003.fastq.gz
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$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 /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq/Paramecium-caudatum-strain_43c3d-vegetative-raw_reads-Lynch508-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 /N/dc2/projects/paramecium/RAW_DATA/Paramecium/caudatum/strain_43c3d/RNA/vegetative/raw_reads/Lynch508-40_S1_L001_R1_001.fastq,/N/dc2/projects/paramecium/RAW_DATA/Paramecium/caudatum/strain_43c3d/RNA/vegetative/raw_reads/Lynch508-44_S1_L001_R1_001.fastq,/N/dc2/projects/paramecium/RAW_DATA/Paramecium/caudatum/strain_43c3d/RNA/vegetative/raw_reads/Lynch508-86_S1_L001_R1_001.fastq /N/dc2/projects/paramecium/RAW_DATA/Paramecium/caudatum/strain_43c3d/RNA/vegetative/raw_reads/Lynch508-40_S1_L001_R2_001.fastq,/N/dc2/projects/paramecium/RAW_DATA/Paramecium/caudatum/strain_43c3d/RNA/vegetative/raw_reads/Lynch508-44_S1_L001_R2_001.fastq,/N/dc2/projects/paramecium/RAW_DATA/Paramecium/caudatum/strain_43c3d/RNA/vegetative/raw_reads/Lynch508-86_S1_L001_R2_001.fastq
cd /N/dc2/projects/marinovg/2015-02-13-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:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/caudatum_43c3d_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/transcriptome-indexes/caudatum_43c3d_annotation_v1 -o /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq/Paramecium-caudatum-strain_43c3d-vegetative-raw_reads-Lynch508D-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_caudatum_43c3d/bowtie-indexes/caudatum_43c3d_assembly_v1 /N/dc2/projects/paramecium/RAW_DATA/Paramecium/caudatum/strain_43c3d/RNA/vegetative/raw_reads/Lynch508D-Paramecium_S8_L001_R1_001.fastq /N/dc2/projects/paramecium/RAW_DATA/Paramecium/caudatum/strain_43c3d/RNA/vegetative/raw_reads/Lynch508D-Paramecium_S8_L001_R2_001.fastq
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$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 /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq/Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1 /N/dc2/projects/paramecium/RAW_DATA/Paramecium/sexaurelia/strain_CA1/RNA/vegetative/110506_IRIS_00020/para3_1_sequence.txt.gz /N/dc2/projects/paramecium/RAW_DATA/Paramecium/sexaurelia/strain_CA1/RNA/vegetative/110506_IRIS_00020/para3_2_sequence.txt.gz
cd /N/dc2/projects/marinovg/2015-02-13-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:$PATH; /N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 16 --no-discordant --no-mixed --microexon-search --read-realign-edit-dist 0 --library-type fr-firststrand --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --min-segment-intron 10 --min-coverage-intron 10 --GTF /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf --transcriptome-index /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/transcriptome-indexes/sexaurelia_AZ8-4_annotation_v1 -o /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq/Paramecium-sexaurelia-strain_CA1-vegetative-141105-6V-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/bowtie-indexes/sexaurelia_AZ8-4_assembly_v1 /N/dc2/projects/paramecium/RAW_DATA/Paramecium/sexaurelia/strain_CA1/RNA/vegetative/141105/6V_ATGTCAGA_L001_R1_001.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Paramecium/sexaurelia/strain_CA1/RNA/vegetative/141105/6V_ATGTCAGA_L001_R3_001.fastq.gz
cd /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq; export PATH=/N/dc2/projects/marinovg/programs/bowtie-0.12.9:/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64:$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 /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq/Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 /N/dc2/projects/paramecium/RAW_DATA/Paramecium/tetraurelia/strain_unknown_1/RNA/vegetative/110506_IRIS_00020/para4_1_sequence.txt.gz /N/dc2/projects/paramecium/RAW_DATA/Paramecium/tetraurelia/strain_unknown_1/RNA/vegetative/110506_IRIS_00020/para4_2_sequence.txt.gz
cd /N/dc2/projects/marinovg/2015-02-13-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 /N/dc2/projects/marinovg/2015-02-13-Paramecium-RNA-seq/Paramecium-tetraurelia-strain_unknown_1-vegetative-141105-4V-TopHat-2.0.8-minIntron10 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tetraurelia.GCA_000165425/bowtie-indexes/Paramecium_tetraurelia.GCA_000165425.1.20 /N/dc2/projects/paramecium/RAW_DATA/Paramecium/tetraurelia/strain_unknown_1/RNA/vegetative/141105/4V_AGTTCCGT_L001_R1_001.fastq.gz,/N/dc2/projects/paramecium/RAW_DATA/Paramecium/tetraurelia/strain_unknown_1/RNA/vegetative/141105/4V_AGTTCCGT_L001_R1_002.fastq.gz /N/dc2/projects/paramecium/RAW_DATA/Paramecium/tetraurelia/strain_unknown_1/RNA/vegetative/141105/4V_AGTTCCGT_L001_R3_001.fastq.gz,/N/dc2/projects/paramecium/RAW_DATA/Paramecium/tetraurelia/strain_unknown_1/RNA/vegetative/141105/4V_AGTTCCGT_L001_R3_002.fastq.gz