Question: Different alignments rates with bwa mem (0%) and bowtie2 (82%)
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gravatar for James Ashmore
2.1 years ago by
James Ashmore2.6k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore2.6k wrote:

I have ChIP-seq data which has been trimmed using trim galore (all default settings). When I align these trimmed reads using bwa mem (all default settings) I get no aligned reads, but when I use bowtie2 (all default settings) I get an 82% alignment rate. The trimmed reads are ~20 bp in length. The run time with bwa is a lot faster than bowtie2 so I think maybe bwa is discarding reads based on some internal quality or length filter.

Below is the samtools flagstat output for bwa mem:

4476553 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 mapped (0.00% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

and for bowtie2:

4476553 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
3696458 + 0 mapped (82.57% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
bwa bowtie2 • 1.2k views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by James Ashmore2.6k

you may find some interesting suggestions here When and why is bwa aln better then bwa mem? and here http://seqanswers.com/forums/showthread.php?t=15200

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by vmicrobio240

try mapping only the longest reads. BWA mem has default minimum seed length as 19. But anyways mem is not the right option for very short reads, I would stick with the bwa aln if not bowtie2

ADD REPLYlink written 2.1 years ago by stolarek.ir580

bwa mem default minimum seed length is 20 bp (or 19 bp?). If none of your reads exceed that length, then the seed alignments obviously can't be extended..

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by 5heikki8.3k

According to the default, the seed length is 19bp. The minimum read length I have is 20bp and the longest is 26bp. I'll try a seed length of 10 and see if that increases the alignment rate.

Edit:

No improvement setting the initial seed length to 10 bp. Still a 0% alignment rate with bwa.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by James Ashmore2.6k
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