Closed caleblareau closed 6 years ago
Sample .bam
below
Difference between MD:A and MD:Z on page 7 of the samtools pdf
Hi Caleb,
That sounds like a reasonable idea, I can probably take a look at this next week. Which aligner are you using, out of interest?
I am afraid the test file you linked comes up with videos of ladies who don't seem to be appropriately dressed for this time of year, and lots of "access blocked" warnings. I could provide you with a link to an FTP site to upload the file if that would help? In addition, I would also need a SNP file which you are using for the the SNPsplit process.
Yeesh, sorry about the link... I didn't see any suspicious behavior from my end; that's quite embarrassing.
Here's a google drive link: https://drive.google.com/file/d/1pDl6seq6k_bIWyzKNVGz5r866FUWr5md/view?usp=sharing
I'm using bowtie2
with a -X 2000
flag, which I think is the only reason that I can align some small fragments (8, 9 bp). These come from the fact that I'm parsing out some scATAC-seq data where one read is heavily barcoded, and after trimming it, can be quite small. However, the paired read is still 36 bp, so I suspect bowtie2 is able to figure out how to align these very short reads when they arise. Note, though, these are exceptions and not the rules.
Thanks again!
Hi Caleb,
That link worked much better.... I managed to download the BAM file (you didn't supply a SNP file though) and had a quick look. There was indeed one read which had an MD:A
tag but no MD:Z:
tag. I also noticed that you used Bowtie2 version 2.2.2
which is nearly 4 years old! Would you mind upgrading Bowtie2 to see if the problem still exists (which I doubt it does). I would like to avoid chasing red herrings that might have been fixed on the Bowtie2 side years ago. Cheers, Felix
Is there any update on this?
Assuming this has been fixed.
Hi @FelixKrueger,
Great tool; quick question-- I get some reads with a
MD:A
tag (see attached .bam file), which causes SNPsplit to fail. My understanding though is that one could still use this tag as it specifies a character instead of a string: https://samtools.github.io/hts-specs/SAMv1.pdfAny thoughts to change the regex to include MD:A: tags? https://github.com/FelixKrueger/SNPsplit/blob/7bed7b64877986d9de599244a27c87a3d66a146e/SNPsplit#L236
On this note, I think that a more-graceful bow-out would be just leaving reads without an MD:Z tag as unassigned rather than killing the whole script. I don't know if you have thoughts on this?
Thanks, -Caleb