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-   -   Error message when uploading a file into UCSC genome browser (http://seqanswers.com/forums/showthread.php?t=17676)

petrosul 02-14-2012 10:21 AM

Error message when uploading a file into UCSC genome browser
 
Hi. I used QuEST to find peaks in my ChIP-seq data. It looks good, found 4000 peaks with minimum enrichment of 15. But when I try to upload a calls.filtered.bed file into genome browser, I see this error message:
"File 'ChIP_calls.filtered.bed' - Error line 3536 of custom track: chromStart after chromEnd (-1 > 3)". The other calls file from a different sample uploads into the browser just fine. I tried to rerun QuEST, but still get the same message uploading this file.

GW_OK 02-14-2012 10:59 AM

did you try looking at line 3536 of the bed file?

ETHANol 02-14-2012 11:08 AM

The UCSC genome browser doesn't like reads that map off the ends of chromosomes or negative numbers. You can run this little script I wrote on your file or since it is so small just open it up with a text editor and fix the offending line.

http://sourceforge.net/projects/etha...dRepair.pl.gz/


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