Hi Duke,
You can also use samtools and perl can make a wiggle ascii directly from the
BAM file:
samtools pileup my.bam \
| perl -pe '($c, $start, undef, $depth) = split; \
if ($c ne $lastC || $start != $lastStart+1) { \
print "fixedStep chrom=$c start=$start step=1 span=1\n"; \
} \
$_ = "$depth\n"; \
($lastC, $lastStart) = ($c, $start);' \
| gzip -c > my.fixedStep.gz
Then use wigToBigWig on my.fixedStep.gz to create a bigWig.
I hope this information is helpful to you. Please don't hesitate to contact us
again if you require further assistance.
Best,
Mary Goldman
UCSC Genome Bioinformatics Group
----- Original Message -----
From: "Hiram Clawson" <[email protected]>
To: "Duke" <[email protected]>
Cc: [email protected]
Sent: Wednesday, December 1, 2010 10:53:33 AM GMT -08:00 US/Canada Pacific
Subject: Re: [Genome] BAM always in "dense"
If your track has too many items in one location, it can't be displayed
in anything but dense or squish. Create a wiggle track of the density
of the overlaps with the kent program: bedItemOverlapCount in order
to get a picture of the pile ups.
---Hiram
----- Original Message -----
From: "Duke" <[email protected]>
To: [email protected]
Sent: Wednesday, December 1, 2010 10:40:24 AM GMT -08:00 US/Canada Pacific
Subject: Re: [Genome] BAM always in "dense"
Any one?
I currently have few tracks with the same issues (they are in squish,
but they look like just dense) on our local mirror. I wonder it is our
local mirror, or it is how it happens.
Thanks,
D.
On 11/30/10 5:14 PM, Duke wrote:
> Hi all,
>
> Please correct me if I am wrong. Is the UCSC browser working with the
> BAM files as if there are too many data to show, these BAM tracks will
> always be in "dense" no matter what type (squish, full) you have chosen
> the tracks to be?
>
> Thanks,
>
> D.
_______________________________________________
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https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
