TopHat - wig file not compatible with UCSC?

dukevn · 11-25-2009, 12:14 PM

Hi all,

I tried TopHat (http://tophat.cbcb.umd.edu/) and got outputs including both bed and wig files. With custom track on UCSC, junctions.bed was loaded without any problem. But when I tried with coverage.wig file, I always got error:

Error File 'coverage.wig' - Error line 2003840 of custom track: chromEnd less than 1 (0)

Anybody sees this error before?

Thanks,

D.

HTS · 11-25-2009, 01:59 PM

Yes, I got the same error and have reported the bug to Cole Trapnell. Try to look for the line says "chrM 0 0 0" and delete it, and it should solve the problem (at least it works in my case).

-- Leo

Kasycas · 11-30-2009, 07:37 AM

Hi,

I have the same problem. Did Leo's solution work for you dukevn?

Thanks!

dukevn · 11-30-2009, 07:53 AM

Quote:

Originally Posted by Kasycas

Hi,

I have the same problem. Did Leo's solution work for you dukevn?

Thanks!

Yes, it worked for me as well. Thanks for your temp solution Leo.

D.

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11-25-2009, 12:14 PM	#1
dukevn Member Location: RI Join Date: Apr 2009 Posts: 50	TopHat - wig file not compatible with UCSC? Hi all, I tried TopHat (http://tophat.cbcb.umd.edu/) and got outputs including both bed and wig files. With custom track on UCSC, junctions.bed was loaded without any problem. But when I tried with coverage.wig file, I always got error: Error File 'coverage.wig' - Error line 2003840 of custom track: chromEnd less than 1 (0) Anybody sees this error before? Thanks, D.

11-30-2009, 07:37 AM	#3
Kasycas Member Location: Dublin, Ireland Join Date: Sep 2009 Posts: 22	same problem Hi, I have the same problem. Did Leo's solution work for you dukevn? Thanks!

11-25-2009, 01:59 PM	#2
HTS Member Location: Toronto Join Date: Nov 2009 Posts: 24	Yes, I got the same error and have reported the bug to Cole Trapnell. Try to look for the line says "chrM 0 0 0" and delete it, and it should solve the problem (at least it works in my case). -- Leo