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dariober / SICERpy

Python wrapper around the popular ChIP-Seq peak caller SICER
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remove redundant reads threshold #9

Closed dinovski closed 6 years ago

dinovski commented 6 years ago

Why has the option to remove redundant reads been commented out?

dariober commented 6 years ago

Hi- sorry I couldn't reply earlier. Can you point me to the part that has been commented out? Your question doesn't have enough information for me to understand what the issue is.

dinovski commented 6 years ago

Hi, lines 122 and 156-158 are commented out in SICER.py so the read threshold argument is not functional.

dariober commented 6 years ago

Hi- If you look at line 135 and 140 in SICER.py, you can see that the read threshold args.redThresh is passed to the script remove_redundant_reads_bam.py. So yes, args.redThresh is still used.

If you notice anything weird I'll investigate further how remove_redundant_reads_bam.py uses the --threshold argument (although remove_redundant_reads_bam.py comes from the original source of SICER)