/users/ldicroce/eblanco/molbio/bin/tophat --no-coverage-search -p 4 -g 1 -G /no_backup/ldicroce/eblanco/molbio/indexes/mm10/refGene.gtf -o /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593 /no_backup/ldicroce/eblanco/molbio/indexes/mm10/genome rawdata/114W1_08593.fastq.gz
/nfs/users/ldicroce/eblanco/molbio/bin/gtf_juncs /no_backup/ldicroce/eblanco/molbio/indexes/mm10/refGene.gtf  > /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/refGene.juncs
#>prep_reads:
/nfs/users/ldicroce/eblanco/molbio/bin/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/ --max-multihits 1 --max-seg-multihits 10 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p4 --gtf-annotations /no_backup/ldicroce/eblanco/molbio/indexes/mm10/refGene.gtf --gtf-juncs /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/refGene.juncs --no-closure-search --no-coverage-search --no-microexon-search --aux-outfile=/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/prep_reads.info --index-outfile=/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.bam.index --sam-header=/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/genome_genome.bwt.samheader.sam --outfile=/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.bam rawdata/114W1_08593.fastq.gz
#>map_start:
/nfs/users/ldicroce/eblanco/molbio/bin/gtf_to_fasta --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/ --max-multihits 1 --max-seg-multihits 10 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p4 --gtf-annotations /no_backup/ldicroce/eblanco/molbio/indexes/mm10/refGene.gtf --gtf-juncs /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/refGene.juncs --no-closure-search --no-coverage-search --no-microexon-search /no_backup/ldicroce/eblanco/molbio/indexes/mm10/refGene.gtf /no_backup/ldicroce/eblanco/molbio/indexes/mm10/genome.fa /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/refGene.fa > /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/logs/g2f.out
/nfs/users/ldicroce/eblanco/molbio/bin/bowtie-build /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/refGene.fa /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/refGene
/nfs/users/ldicroce/eblanco/molbio/bin/bam2fastx --all /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.bam|/nfs/users/ldicroce/eblanco/molbio/bin/bowtie -v 2 -k 60 -m 60 -S -p 4 --sam-nohead --max /dev/null /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/refGene -|/nfs/users/ldicroce/eblanco/molbio/bin/fix_map_ordering --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --bowtie1 --sam-header /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/refGene.bwt.samheader.sam - - /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um.bam | /nfs/users/ldicroce/eblanco/molbio/bin/map2gtf --sam-header /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/genome_genome.bwt.samheader.sam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/refGene.fa.tlst - /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g.bam > /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/logs/m2g_left_kept_reads.out
/nfs/users/ldicroce/eblanco/molbio/bin/bam2fastx --all /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um.bam|/nfs/users/ldicroce/eblanco/molbio/bin/bowtie -v 2 -k 1 -m 1 -S -p 4 --sam-nohead --max /dev/null /no_backup/ldicroce/eblanco/molbio/indexes/mm10/genome -|/nfs/users/ldicroce/eblanco/molbio/bin/fix_map_ordering --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um.mapped.bam.index --bowtie1 --sam-header /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/genome_genome.bwt.samheader.sam - /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um.mapped.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_unmapped.bam
#>map_segments:
gzip -cd< /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg1.fq.z|/nfs/users/ldicroce/eblanco/molbio/bin/bowtie -v 2 -k 10 -m 10 -S -p 4 --sam-nohead --max /dev/null /no_backup/ldicroce/eblanco/molbio/indexes/mm10/genome -|/nfs/users/ldicroce/eblanco/molbio/bin/fix_map_ordering --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg1.bam.index --bowtie1 --sam-header /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/genome_genome.bwt.samheader.sam - /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg1.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg1_unmapped.bam
gzip -cd< /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg2.fq.z|/nfs/users/ldicroce/eblanco/molbio/bin/bowtie -v 2 -k 10 -m 10 -S -p 4 --sam-nohead --max /dev/null /no_backup/ldicroce/eblanco/molbio/indexes/mm10/genome -|/nfs/users/ldicroce/eblanco/molbio/bin/fix_map_ordering --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg2.bam.index --bowtie1 --sam-header /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/genome_genome.bwt.samheader.sam - /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg2.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg2_unmapped.bam
#>find_juncs:
/nfs/users/ldicroce/eblanco/molbio/bin/segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/ --max-multihits 1 --max-seg-multihits 10 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p4 --gtf-annotations /no_backup/ldicroce/eblanco/molbio/indexes/mm10/refGene.gtf --gtf-juncs /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/refGene.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/genome_genome.bwt.samheader.sam --ium-reads /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg1_unmapped.bam,/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg2_unmapped.bam /no_backup/ldicroce/eblanco/molbio/indexes/mm10/genome.fa /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/segment.juncs /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/segment.insertions /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/segment.deletions /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/segment.fusions /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um.mapped.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg1.bam,/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg2.bam
#>juncs_db:
/nfs/users/ldicroce/eblanco/molbio/bin/juncs_db 3 25 /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/refGene.juncs,/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/segment.juncs /dev/null /dev/null /dev/null /no_backup/ldicroce/eblanco/molbio/indexes/mm10/genome.fa > /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/segment_juncs.fa
/nfs/users/ldicroce/eblanco/molbio/bin/bowtie-build /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/segment_juncs.fa /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/segment_juncs
#>map2juncs:
gzip -cd< /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg1.fq.z|/nfs/users/ldicroce/eblanco/molbio/bin/bowtie -v 2 -k 10 -m 10 -S -p 4 --sam-nohead --max /dev/null /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/segment_juncs -|/nfs/users/ldicroce/eblanco/molbio/bin/fix_map_ordering --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam.index --bowtie1 --sam-header /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/segment_juncs.bwt.samheader.sam - /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam
gzip -cd< /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg2.fq.z|/nfs/users/ldicroce/eblanco/molbio/bin/bowtie -v 2 -k 10 -m 10 -S -p 4 --sam-nohead --max /dev/null /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/segment_juncs -|/nfs/users/ldicroce/eblanco/molbio/bin/fix_map_ordering --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam.index --bowtie1 --sam-header /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/segment_juncs.bwt.samheader.sam - /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam
/nfs/users/ldicroce/eblanco/molbio/bin/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/ --max-multihits 1 --max-seg-multihits 10 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p4 --gtf-annotations /no_backup/ldicroce/eblanco/molbio/indexes/mm10/refGene.gtf --gtf-juncs /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/refGene.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/genome_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 /no_backup/ldicroce/eblanco/molbio/indexes/mm10/genome.fa /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/refGene.juncs,/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/segment.juncs /dev/null /dev/null /dev/null /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um.candidates.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg1.bam,/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg2.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bam,/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bam
#>tophat_reports:
/nfs/users/ldicroce/eblanco/molbio/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/ --max-multihits 1 --max-seg-multihits 10 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --bowtie1 -z gzip -p4 --gtf-annotations /no_backup/ldicroce/eblanco/molbio/indexes/mm10/refGene.gtf --gtf-juncs /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/refGene.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/nfs/users/ldicroce/eblanco/molbio/bin/samtools_0.1.18 --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 /no_backup/ldicroce/eblanco/molbio/indexes/mm10/genome.fa /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/junctions.bed /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/insertions.bed /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/deletions.bed /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/fusions.out /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/accepted_hits /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g.bam,/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um.mapped.bam,/no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.m2g_um.candidates /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/left_kept_reads.bam
/nfs/users/ldicroce/eblanco/molbio/bin/samtools_0.1.18 sort /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/accepted_hits0.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/accepted_hits0_sorted
/nfs/users/ldicroce/eblanco/molbio/bin/samtools_0.1.18 sort /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/accepted_hits1.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/accepted_hits1_sorted
/nfs/users/ldicroce/eblanco/molbio/bin/samtools_0.1.18 sort /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/accepted_hits2.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/accepted_hits2_sorted
/nfs/users/ldicroce/eblanco/molbio/bin/samtools_0.1.18 sort /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/accepted_hits3.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/accepted_hits3_sorted
/nfs/users/ldicroce/eblanco/molbio/bin/samtools_0.1.18 merge -f -h /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/genome_genome.bwt.samheader.sam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/accepted_hits.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/accepted_hits0_sorted.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/accepted_hits1_sorted.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/accepted_hits2_sorted.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/accepted_hits3_sorted.bam
/nfs/users/ldicroce/eblanco/molbio/bin/bam_merge -Q --sam-header /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/genome_genome.bwt.samheader.sam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/unmapped.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/unmapped_left_0.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/unmapped_left_1.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/unmapped_left_2.bam /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W1_08593/tmp/unmapped_left_3.bam
#>alldone: