wig files to bigwig using UCSC kent
Hello! I am trying to convert wig files to bigwig using UCSC kent module -
grep -hv 'track' in.wig > 1.wig
sed '1d' 1.wig > 2.wig
wigToBigWig 2.wig -clip chrom.sizes 2.bw
I get the error - hashMustFindVal: 'chr2CEN' not found
I don't think this is a genome version error, I tried the most current and a previous version and still get the error.
I already looked for answers in -
bedGrapthToBigWig conversion, xxx is not found in chromosome files
Has anyone else faced this? Please let me know, thank you for your help!
You need to make sure that all of the chromosome names in your wiggle file are accounted for in the chrom.sizes file.
For instance, if my wiggle file looks like this:
And my chrom.sizes file looks like this:
Then I can still run wigToBigWig just fine:
wigToBigWig test1.wig test.chrom.sizes out1.bw
Now whether that wiggle will actually display in the genome browser is a different story, but it seems to me that your wiggle just has incorrect chromosome names and needs to be fixed.
If you have further questions about UCSC data or tools feel free to send your question to one of the below mailing lists:
- General questions: email@example.com
- Questions involving private data: firstname.lastname@example.org
- Questions involving mirror sites:
ChrisL from the UCSC Genome Browser
Traffic: 1577 users visited in the last hour