Question: bigwig file can see in igv but not in ucsc
0
gravatar for yuxinghai
3.6 years ago by
yuxinghai10
yuxinghai10 wrote:

I use bam2wig covert sam files into bigwig files, and peaks can be seen in igv but shown no data in ucsc. I'm wondering what happened? And my bigwig file size is about 700M.

igv rna-seq ucsc • 1.5k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by yuxinghai10
1
gravatar for Pierre Lindenbaum
3.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum130k wrote:

did you use the same chromosome names ('chr' prefix) than in the UCSC browser ?

ADD COMMENTlink written 3.6 years ago by Pierre Lindenbaum130k

Thanks your answer, my bigwig file chromosome names only start with number, but i don't know how to make it work.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by yuxinghai10
  • convert you bigwig to wig using the UCSC tools bigWigToWig
  • use sed to change the chromosome names using sed . eg.:

    sed 's/chrom=/chrom=chr/'

  • move the resulting wiggle file to bigwig using wigToBigWig

ADD REPLYlink written 3.6 years ago by Pierre Lindenbaum130k

Dose there any mothod don't have to covert bigwig to wig? can you help me?

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by yuxinghai10

you could convert the name in the original bam : Bam File: Change Chromosome Notation

ADD REPLYlink written 3.6 years ago by Pierre Lindenbaum130k

it works,Thank you for your help!

ADD REPLYlink written 3.6 years ago by yuxinghai10
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