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Old 02-14-2012, 09:21 AM   #1
petrosul
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Location: boulder

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Default 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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Old 02-14-2012, 09:59 AM   #2
GW_OK
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did you try looking at line 3536 of the bed file?
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Old 02-14-2012, 10:08 AM   #3
ETHANol
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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/
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