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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!
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!