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yezhengSTAT / mHiC

MIT License
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*.UNI file missing #3

Closed Lila14 closed 6 years ago

Lila14 commented 6 years ago

Line 33 of s4_bin.sh uses a file $validP.UNI as input. But this file doesn't exist (/data/drive1/hic_data/mhic/GM12878/GM12878_rep1.validPairs.UNI on my system) and I can't figure out which step is supposed to generate it.

yezhengSTAT commented 6 years ago

Hi Lila, Yes, you are right. I was confused by the new version of s4_bin.sh with the old one that is on github right now and I have commented that command. The updated version which generates $validP.UNI will have a faster sorting, better duplicates removal algorithm, and much faster normalization. I am testing it on high resolution on GM12878 cell line and will post it once it proves to be stable.

yezhengSTAT commented 6 years ago

Hi Lila, I just updated the pipeline with a relatively recent s4_bin.sh (the ultra new one is still under test). If you are not running GM12878 at extremely high resolution, the updated version should be able to handle it. :)

Best, Ye

yezhengSTAT commented 6 years ago

Hi Lila, Finally, the newest s4_bin.sh that can deal with high-resolution Hi-C matrix normalization (KR method) is out there. Thanks for pointing out the bugs in the pipeline!

Ye