Great! Thanks Mary and Hiram. At least I know that there is nothing
wrong with our local mirror.
Thanks,
D.
On 12/1/10 2:11 PM, Mary Goldman wrote:
> 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.
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
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