Question: Troubleshooting MACS bdgcmp
gravatar for mparker2
5.7 years ago by
mparker220 wrote:

I am trying to generate a log FE Bedgraph file from some chip seq data. I already have some bedgraph tracks for the control and treated samples, but when I run MACS bdgcmp for the two I get an error message. Can anyone enlighten me as to how to fix this:

macs2 bdgcmp -t /home/matthew/Desktop/Projects/raw_data/histone_chip/HTR5_treat_afterfiting_all.bdg.gz -c /home/matthew/Desktop/Projects/raw_data/histone_chip/HTR5_control_afterfiting_all.bdg.gz --outdir /home/matthew/Desktop/Projects/raw_data/histone_chip/ --o-prefix HTR5_FE -m logFE
INFO  @ Fri, 19 Jun 2015 14:48:14: Read and build treatment bedGraph...
Traceback (most recent call last):
  File "/usr/local/bin/macs2", line 4, in <module>
    __import__('pkg_resources').run_script('MACS2==', 'macs2')
  File "build/bdist.linux-x86_64/egg/pkg_resources/", line 729, in run_script
  File "build/bdist.linux-x86_64/egg/pkg_resources/", line 1649, in run_script
  File "/usr/local/lib/python2.7/dist-packages/MACS2-", line 614, in <module>
  File "/usr/local/lib/python2.7/dist-packages/MACS2-", line 72, in main
  File "build/bdist.linux-x86_64/egg/MACS2/", line 40, in run
  File "MACS2/IO/BedGraphIO.pyx", line 108, in MACS2.IO.BedGraphIO.bedGraphIO.build_bdgtrack (MACS2/IO/BedGraphIO.c:1245)
IndexError: list index out of range


chip-seq • 2.1k views
ADD COMMENTlink written 5.7 years ago by mparker220
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