Circular chromosomes

[Vince]

Hi,

Would it be possible to have bedtools genomecov deal with circular
chromosomes? It doesn't like ie mitochondrial input that crosses 0.
This isn't a huge priority for me since I should be able to grep out
the offending input and don't need MT information at the moment, but
it seems like it would be useful.

Thanks,

Vince

[Vince]

One more tidbit...

I used a command like
bamToBed -i seq.alnSDU.bam | slopBed -s -r 75 -l 0 -i stdin -g
$genomefile | genomeCoverageBed -bga -scale 0.03049 -i stdin -g
$genomefile > seq.bgr

and I would have thought that this would generate clean trimmed input
for genomeCoverageBed. genomeCoverageBed didn't like this line of
input:
MT 0 -1 9432NS1:23:C0YBUACXX:3:1105:8122:35974/2 29 +
So it looks like slopBed is causing the problem with this input
MT 0 20 9432NS1:23:C0YBUACXX:3:1105:8122:35974/2 29 +

Vince

[Vince]

One last update, sorry about the flurry of email...

It looks like the slopbed problem is caused by my incorrect
chromosomes file, which was missing the MT chromosome (actually had it
as M not MT). So slopBed gives a -1 as end position if the chromosome
is missing from the chromosome file?

Vince

[Aaron Quinlan]

Hi Vince,

Thanks for reporting this, I will look into what might be happening if there is no chrom entry in the genome file.

Also, in the short term it will be a bit difficult to support circular chromosomes.  As such, I would suggest filtering the data out if it is sensible for your analysis.

Thanks and sorry for the delayed response.

- Aaron

quinlanlab.org

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