Possible to convert chromosome names on bigWig file?

[Harold Pimentel]

Hi all,

I have some bigWig coverage files made from bed graph files (which were made from genomeCoverageBed on some BAM files) and I'm trying to view them on the genome browser. The original data was mapped to the Ensembl version of the human  genome. Interestingly, the reads show up correctly on a browser track even though the chromosome names do not match in the BAM files (i.e. 1 vs chr1). Unfortunately, the same is not true for the bigWig files and the track displays completely empty on the genome browser. Is there something I can change on the browser to properly display this track?

If not, is there an easy way to convert the chromosome names on the bigWig file to match the genome browser?

Thanks!

Harold

[Luvina Guruvadoo]

Hello Harold,

Thank you for contacting us. In order to display the chromosome names
correctly, you will have to go back to your bed file used to construct
the bigWig file and change the chromosome names, then construct a new
bigWig file. One of our engineers suggests using a sed command similar
to the one below to convert Ensembl GRCh37 names to UCSC hg19 names:

's/^\([0-9XY][0-9]*\)/chr\1/; s/^MT/chrM/; /^GL3.*/d; /^HSCHR[1-5]/d;
/^HSCHR[7-9]/d;
/^HSCHR6_1/d; /^HG/d'

If you have any further questions, please reply to
gen...@soe.ucsc.edu. All messages sent to that address are archived on
a publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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