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makebigwigfiles bedtools genomecov error #1

Closed Enidanellani closed 5 years ago

Enidanellani commented 5 years ago

Hello eclip team!

I'm trying to use your pipeline for single-end eclip analysis which I got from github. However, when I try to run the small example you provide (cwl-runner ../cwl/wf_get_peaks_scatter_se.cwl single_end_clip_small.yaml), I obtain the following error when making bigwig files: ERROR: Unrecognized parameter: -du This error is related to the bedtools genomecov function called in one of the make_bigwig_files.py scripts. In one of these scripts, the "-du" flag is called, although bedtools genomecov does not have this option. When I went through the make_bigwig_files.py scipts in my environment (/envs/clip-seq/lib/python2.7/site-packages/gscripts-0.1.6-py2.7.egg/gscripts/general/make_bigwig_files.py or envs/clip-seq/lib/python2.7/site-packages/gscripts-0.1.6-py2.7.egg/EGG-INFO/scripts/make_bigwig_files.py) I cannot find the "-du" flag. However, the same script in your github repository (https://github.com/YeoLab/makebigwigfiles/blob/master/makebigwigfiles/make_bigwig_files.py) shows the "-du" option which needs to be removed. Could you please indicate where I find the make_bigwig_files.py script is located that is called by the program, so I can manually remove the "-du" which will most probably solve my issue. Thank you so much for your help! All the best, Nina

byee4 commented 5 years ago

Which version of bedtools are you using? Bedtools 2.27.1 should have the -du flag available

Enidanellani commented 5 years ago

Hi! Thanks for your quick answer! I am using bedtools version 2.25.0 (as defined in the create_environment_clipseq.sh file). I upgraded to 2.27.1 and it works now, thank you so much! However, I cannot find the -du option in any bedtools documentation. What does it mean? All the best, Nina

byee4 commented 5 years ago

bedtools genomecov: 

-du             Change strand af the mate read (so both reads from the same strand) useful for strand specific
                        Works for BAM files only

Thanks for letting us know about the version discrepancy, we'll update the documentation.