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Old 12-02-2017, 02:20 PM   #1
__sequence
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Location: EU

Join Date: Jun 2011
Posts: 13
Default MACS2 output on Galaxy not readbale by BedTools on Galaxy

Hi!

I am getting the following error with Galaxy (need to get an answer specifically for Galaxy; without Galaxy I am not getting this error):

I am running MACS2.1.0 in galaxy to determine narrow peaks in ChIP-seq. The file looks OK. Then I start BedTools using the output from Galaxy as input to BedTools, and it does not work. Note, that BedTools works absolutely fine with the same commands when I am using as input another BED file uploaded to galaxy from my PC. So there is some specific problem with the MACS2.1.0 output.

The craziest thing is that when I try using the MACS2.1.0 output as input for BedTools, it not only gives an error, but also corrupts the BED file with MACS peaks.

Anyone encountered this glitch?

Thanks!
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