/data/results/tools/align/bowtie-0.12.9/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c -C -v 2 -m 10 --best --strata -q 0hrep1.fastq  > 0hrep1.bowtie
# reads processed: 8276787
# reads with at least one reported alignment: 131225 (1.59%)
# reads that failed to align: 8130027 (98.23%)
# reads with alignments suppressed due to -m: 15535 (0.19%)
Reported 131225 alignments to 1 output stream(s)
/data/results/tools/align/bowtie-0.12.9/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c -C -v 2 -m 10 --best --strata -q 0hrep2.fastq  > 0hrep2.bowtie
# reads with at least one reported alignment: 101656 (2.43%)
# reads that failed to align: 4073843 (97.28%)
# reads with alignments suppressed due to -m: 12399 (0.30%)
Reported 101656 alignments to 1 output stream(s)
/data/results/tools/align/bowtie-0.12.9/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c -C -v 2 -m 10 --best --strata -q 0hrep3.fastq  > 0hrep3.bowtie
# reads processed: 12168985
# reads with at least one reported alignment: 228422 (1.88%)
# reads that failed to align: 11916860 (97.93%)
# reads with alignments suppressed due to -m: 23703 (0.19%)
Reported 228422 alignments to 1 output stream(s)


#clipped aligment:
/data/results/tools/align/bowtie-1.2.1.1/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c -3 30 -C -v 3 -m 10 --best --strata -f 0hrep1filt2_T_F3.csfasta.coll -S  |samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > 0hrep1F-bt1.bam
#/data/results/tools/align/bowtie-0.12.9/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c -3 30 -C -v 3 -m 10 --best --strata -f 0hrep1filt2_T_F3.csfasta.coll -S ||samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > 0hrep1F-bt1.bam
samtools index !$
/data/results/tools/align/rnaseqmut/rnaseqmut-master/bin/rnaseqmut.linux.x64 -r /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -m 0 0hrep1F-bt1.bam  | awk -f /data/results/tools/align/rnaseqmut/count-conversions1.awk > 0hrep1F-bt1.conversion.stats

reczko@max:/data/images/proton/DKlab/mr/parclip/raw$ /data/results/tools/align/bowtie-1.2.1.1/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c -3 30 -C -v 3 -m 10 --best --strata -f 0hrep1filt2_T_F3.csfasta.coll -S  |samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > 0hrep1F-bt1.bam
[bam_header_read] EOF marker is absent. The input is probably truncated.
[samopen] SAM header is present: 22 sequences.
samtools index !$
/data/results/tools/align/rnaseqmut/rnaseqmut-master/bin/rnaseqmut.linux.x64 -r /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -m 0 0hrep1F-bt1.bam  | awk -f /data/results/tools/align/rnaseqmut/count-conversions1.awk > 0hrep1F-bt1.conversion.stats

cat !$
# reads processed: 662129
# reads with at least one reported alignment: 71 (0.01%)
# reads that failed to align: 2 (0.00%)
# reads with alignments suppressed due to -m: 662056 (99.99%)
Reported 71 alignments to 1 output stream(s)
reczko@max:/data/images/proton/DKlab/mr/parclip/raw$ reczko@max:/data/images/proton/DKlab/mr/parclip/raw$ cat 0hrep1F-bt1.conversion.stats
AtoC 1 8.33333
CtoA 1 8.33333
GtoC 1 8.33333
AtoT 1 8.33333
TtoA 7 58.3333
TtoC 1 8.33333
reczko@max:/data/images/proton/DKlab/mr/parclip/raw$ samtools view 0hrep1F-bt1.bam | head
558710-1	0	chr10	20279871	255	18M	*	0	0	TTGTAATGCACTACTTTC	qq!!qqqqqqqqqqqI!I	XA:i:3	MD:Z:18	NM:i:0	CM:i:3	XM:i:2
432597-1	16	chr10	83497212	255	18M	*	0	0	CAGGCTTAGTGTATTATG	I!Iqqqqqqqq!!qqqqq	XA:i:3	MD:Z:18	NM:i:0	CM:i:3	XM:i:2