Unable to view splice junction tracks on ucsc browser

[varsha090597]

Hi,

I ran the junctionseq pipeline and got the Splice Junction Tracks which were generated automatically by the writeCompleteResults. When I tried creating tracks in the ucsc genome browser with these files, I get this error:

Is seems like there is an issue with the input file format, but I am not sure.

Thanks!

[hartleys]

UCSC uses "chr1/chr2/chrX/etc" style chromosome names. So you need to change the chromosome names to match this.

Your chromosomes are in "1/2/X/etc" format (without the "chr"). So you need to add "chr" to the start of each line.

zcat mybedfile.bed.gz | sed 's/^[0-9]/chr/g' | gzip > mybedfile.fixed.bed.gz