/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 -o Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10/ /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf GSF869-Doak-Ugne-209_S7_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-209_S7_R2_001.100mers.fastq.gz
#>prep_reads:
/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 10 --max-report-intron 1000000 --min-isoform-fraction 0.15 --output-dir Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10// --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 10 --max-coverage-intron 20000 --min-segment-intron 10 --max-segment-intron 1000000 --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p16 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --library-type fr-firststrand --fastq --aux-outfile=Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//prep_reads.info --index-outfile=Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/%side%_kept_reads.bam.index --sam-header=Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam --outfile=Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/%side%_kept_reads.bam GSF869-Doak-Ugne-209_S7_R1_001.100mers.fastq.gz GSF869-Doak-Ugne-209_S7_R2_001.100mers.fastq.gz
#>map_start:
/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/bam2fastx --all --fastq Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads.bam|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 3 -k 20 -m 20 -S -p 16 --sam-nohead --max /dev/null /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads.mapped.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads.mapped.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_unmapped.bam
#>map_segments:
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg1.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg1.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg1.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg1_unmapped.bam
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg2.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg2.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg2.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg2_unmapped.bam
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg3.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg3.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg3.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg3_unmapped.bam
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg4.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg4.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg4.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg4_unmapped.bam
/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/bam2fastx --all --fastq Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads.bam|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 3 -k 20 -m 20 -S -p 16 --sam-nohead --max /dev/null /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads.mapped.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads.mapped.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_unmapped.bam
#>map_segments:
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg1.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg1.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg1.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg1_unmapped.bam
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg2.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg2.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg2.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg2_unmapped.bam
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg3.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg3.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg3.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg3_unmapped.bam
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg4.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg4.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg4.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg4_unmapped.bam
#>find_juncs:
/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 10 --max-report-intron 1000000 --min-isoform-fraction 0.15 --output-dir Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10// --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 10 --max-coverage-intron 20000 --min-segment-intron 10 --max-segment-intron 1000000 --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p16 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --library-type fr-firststrand --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam --ium-reads Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg1_unmapped.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg2_unmapped.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg3_unmapped.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg4_unmapped.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg1_unmapped.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg2_unmapped.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg3_unmapped.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg4_unmapped.bam /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf.fa Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment.juncs Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment.insertions Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment.deletions Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment.fusions Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads.mapped.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg1.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg2.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg3.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg4.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads.mapped.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg1.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg2.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg3.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg4.bam
#>juncs_db:
/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/juncs_db 3 25 Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment.juncs Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment.insertions Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment.deletions /dev/null /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf.fa > Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs.fa
/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie-build Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs.fa Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs
#>map2juncs:
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg1.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg1.to_spliced.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg1.to_spliced.bam
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg2.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg2.to_spliced.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg2.to_spliced.bam
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg3.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg3.to_spliced.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg3.to_spliced.bam
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg4.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg4.to_spliced.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg4.to_spliced.bam
/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 10 --max-report-intron 1000000 --min-isoform-fraction 0.15 --output-dir Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10// --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 10 --max-coverage-intron 20000 --min-segment-intron 10 --max-segment-intron 1000000 --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p16 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --library-type fr-firststrand --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf.fa Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment.juncs Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment.insertions Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment.deletions /dev/null Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads.candidates.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg1.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg2.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg3.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg4.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg1.to_spliced.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg2.to_spliced.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg3.to_spliced.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads_seg4.to_spliced.bam
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg1.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg1.to_spliced.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg1.to_spliced.bam
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg2.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg2.to_spliced.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg2.to_spliced.bam
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg3.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg3.to_spliced.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg3.to_spliced.bam
gzip -cd< Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg4.fq.z|/N/dc2/projects/marinovg/programs/bowtie-0.12.9/bowtie -q -v 2 -k 40 -m 40 -S -p 16 --sam-nohead --max /dev/null Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs -|/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/fix_map_ordering --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --index-outfile Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg4.to_spliced.bam.index --bowtie1 --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment_juncs.bwt.samheader.sam - Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg4.to_spliced.bam
/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 10 --max-report-intron 1000000 --min-isoform-fraction 0.15 --output-dir Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10// --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 10 --max-coverage-intron 20000 --min-segment-intron 10 --max-segment-intron 1000000 --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p16 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --library-type fr-firststrand --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf.fa Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment.juncs Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment.insertions Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/segment.deletions /dev/null Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads.candidates.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg1.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg2.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg3.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg4.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg1.to_spliced.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg2.to_spliced.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg3.to_spliced.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads_seg4.to_spliced.bam
#>tophat_reports:
/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 10 --max-report-intron 1000000 --min-isoform-fraction 0.15 --output-dir Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10// --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 10 --max-coverage-intron 20000 --min-segment-intron 10 --max-segment-intron 1000000 --read-mismatches 4 --read-gap-length 2 --read-edit-dist 4 --read-realign-edit-dist 0 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p16 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --library-type fr-firststrand --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam --samtools=/N/soft/rhel6/samtools/0.1.18/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_tredecaurelia_209_CA2/bowtie-indexes/tredecaurelia_209_CA2.scf.fa Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//junctions.bed Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//insertions.bed Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//deletions.bed Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//fusions.out Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads.mapped.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads.candidates Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/left_kept_reads.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads.mapped.bam,Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads.candidates Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/right_kept_reads.bam
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits0.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits0_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits1.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits1_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits2.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits2_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits3.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits3_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits4.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits4_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits5.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits5_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits6.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits6_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits7.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits7_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits8.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits8_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits9.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits9_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits10.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits10_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits11.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits11_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits12.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits12_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits13.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits13_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits14.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits14_sorted
/N/soft/rhel6/samtools/0.1.18/samtools sort Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits15.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits15_sorted
/N/soft/rhel6/samtools/0.1.18/samtools merge -f -h Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//accepted_hits.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits0_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits1_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits2_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits3_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits4_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits5_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits6_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits7_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits8_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits9_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits10_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits11_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits12_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits13_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits14_sorted.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/accepted_hits15_sorted.bam
/N/dc2/projects/marinovg/programs/tophat-2.0.8.Linux_x86_64/bam_merge -Q --sam-header Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/tredecaurelia_209_CA2.scf_genome.bwt.samheader.sam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//unmapped.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_0.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_0.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_1.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_1.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_2.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_2.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_3.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_3.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_4.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_4.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_5.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_5.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_6.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_6.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_7.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_7.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_8.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_8.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_9.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_9.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_10.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_10.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_11.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_11.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_12.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_12.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_13.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_13.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_14.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_14.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_left_15.bam Paramecium_tredecaurelia-GSF869-Doak-Ugne-209_S7-2x100-TopHat-2.0.8-minIntron10//tmp/unmapped_right_15.bam
#>alldone: