/data/results/tools/align/bowtie-0.12.9/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c -p 10 -C -v 2 -m 10 -S --best --strata -f ../Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_9_F3.csfasta -Q /data/images/proton/DKlab/polysomes/reads/Backup_Polysomes_TTP/ugc_623_BC_FRAG_W_Paulina_150506_L02_ugc_623_9_F3.QV.qual  |samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > 0hrep1.bam
/data/results/tools/align/bowtie-0.12.9/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c -p 10 -C -v 2 -m 10 -S --best --strata  ../fastq/0hrep1b.fastq  |samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > 0hrep1b2.bam
# reads processed: 28066949
# reads with at least one reported alignment: 1694297 (6.04%)
# reads that failed to align: 25709002 (91.60%)
# reads with alignments suppressed due to -m: 663650 (2.36%)
Reported 1694297 alignments to 1 output stream(s)

#@stranded nofw
/data/results/tools/align/bowtie-0.12.9/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c --fr --nofw -p 10 -C -v 2 -m 10 -S --best --strata  ../fastq/0hrep1b.fastq  |samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > 0hrep1b2-fr.bam

#@stranded norc
/data/results/tools/align/bowtie-0.12.9/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c --fr --norc -p 10 -C -v 2 -m 10 -S --best --strata  ../fastq/0hrep1b.fastq  |samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > 0hrep1b2-fr-norc.bam