Question: how can I see the coverage of my own BED file on UCSC Genome Browser?
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gravatar for sustcyucw
22 months ago by
sustcyucw20
sustcyucw20 wrote:

I have several BED file of transcripts, and I want to see the coverage of them like IGV shows. But the IGV always crashed because of the low memory, and the coverage also can't show completely. I loaded my BED file on UCSC Genome Browser as custom tracks, but it only show the distribution of every reads.

rna-seq • 770 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by sustcyucw20
1
gravatar for sustcyucw
22 months ago by
sustcyucw20
sustcyucw20 wrote:

I just found BedGraph Track Format, maybe it can solve my problems.

ADD COMMENTlink written 22 months ago by sustcyucw20

But the IGV always crashed because of the low memory ...

You should probably use indexed binary format, such as bigbed for annotation files or bigwig for coverage files. Those file are smaller than wig/bed/bedgraph files and don't need to be fully loaded in the genome browser, meaning that you save a lot of memory.

ADD REPLYlink written 22 months ago by Carlo Yague4.4k
1

You are on the right track.

Just like Carlo said, now that you have your files in bedGraph format, convert them to bigWig format by using UCSC tool command: bedGraphToBigWig <inputBedGraph file> <chromosome size file> <output.bw>

This should not be memory intensive nor should it take too long to convert.
Load the bigWig file on the (UCSC) browser to view the coverage on a continuous scale.

ADD REPLYlink modified 22 months ago • written 22 months ago by shwethacm200
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