Hi,
I have a problem with bowtie and paired end reads:
A read is being reported as unmapped because its mate can not be mapped.
What am I doing wrong?
I have a test genome:
and two test paired read files with reads taken from genome (m1a,m2a,m1b) and mutated/not matching m2b:
read1:
read2:
When I align each file separately I get expected results (3 matching, one not):
When I align them as paired reads, suddenly m2a does not match anymore. I would have excpected it
to be reported as m2a mapped but mate (m2b) unmapped:
I have a problem with bowtie and paired end reads:
A read is being reported as unmapped because its mate can not be mapped.
What am I doing wrong?
I have a test genome:
Code:
>chr1 AAGCTGGGATCGATGCCACGTAGACGTAGTTTAGTGAAACTGATGATTCCCTGATAGTAGCTGACTGATGGGGCAGTAAAAGTCCCCAGTCAGTTGACCTGAC
read1:
Code:
>m1a TGGGATCGATGCCACGTAGACG >m2a TGGGATCGATGCCACGTAGACG
Code:
>m1b GGGCAGTAAAAGTCCCCAGTCAGTT >m2b GGGCAGTTTTTGTGGGGAGTCAGTT
Code:
@HD VN:1.0 SO:unsorted @SQ SN:chr1 LN:103 @PG ID:Bowtie VN:0.12.5 CL:"bowtie/bowtie-0.12.5/bowtie -f -S genome r1.fasta" m1a 0 chr1 5 255 22M * 0 0 TGGGATCGATGCCACGTAGACG IIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:22 NM:i:0 m2a 0 chr1 5 255 22M * 0 0 TGGGATCGATGCCACGTAGACG IIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:22 NM:i:0
Code:
@HD VN:1.0 SO:unsorted @SQ SN:chr1 LN:103 @PG ID:Bowtie VN:0.12.5 CL:"bowtie/bowtie-0.12.5/bowtie -f -S genome r2.fasta" m1b 0 chr1 71 255 25M * 0 0 GGGCAGTAAAAGTCCCCAGTCAGTT IIIIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:25 NM:i:0 m2b 4 * 0 0 * * 0 0 GGGCAGTTTTTGTGGGGAGTCAGTT IIIIIIIIIIIIIIIIIIIIIIIII XM:i:0
to be reported as m2a mapped but mate (m2b) unmapped:
Code:
@HD VN:1.0 SO:unsorted @SQ SN:chr1 LN:103 @PG ID:Bowtie VN:0.12.5 CL:"bowtie/bowtie-0.12.5/bowtie -f -S -m1 --best --strata --ff genome -1 r1.fasta -2 r2.fasta" m1a 67 chr1 5 255 22M = 71 91 TGGGATCGATGCCACGTAGACG IIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:22 NM:i:0 m1b 131 chr1 71 255 25M = 5 -91 GGGCAGTAAAAGTCCCCAGTCAGTT IIIIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:25 NM:i:0 m2a 77 * 0 0 * * 0 0 TGGGATCGATGCCACGTAGACG IIIIIIIIIIIIIIIIIIIIII XM:i:0 m2b 141 * 0 0 * * 0 0 GGGCAGTTTTTGTGGGGAGTCAGTT IIIIIIIIIIIIIIIIIIIIIIIII XM:i:0
Comment