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02-14-2012, 10:21 AM
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#1 |
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Junior Member
Location: boulder Join Date: Feb 2012
Posts: 2
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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. |
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02-14-2012, 10:59 AM
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#2 |
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Senior Member
Location: Oklahoma Join Date: Sep 2009
Posts: 411
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did you try looking at line 3536 of the bed file?
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02-14-2012, 11:08 AM
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#3 |
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Senior Member
Location: Western Australia Join Date: Feb 2010
Posts: 308
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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/
__________________
-------------- Ethan |
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