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angieyen / ChromDiff

ChromDiff program as described in Yen and Kellis, Nature Communications 2015.
http://compbio.mit.edu/ChromDiff
GNU General Public License v3.0
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Failing to reproduce example #4

Open josruirod opened 6 years ago

josruirod commented 6 years ago

Hello. I believe ChromDiff is still recommended for finding out regions with differential chromatin state and linking it with different expression. I'd like to give it a try, but I have not been able to reproduce the example

After downloading the bed.gz files to statecalls/core and running notes_v2.sh I'm getting the following error when processing each feature: awk: calc_perc.awk: line 138: illegal reference to array genename

And at the end: "awk: cannot open backgrounds/core_gencode_v10/perc_background.txt (No such file or directory)". No files or results are created

I'm going to try to figure it out, but I would appreciate any thougths. Thanks

rtmag commented 5 years ago

Hello, I ran into the same issue! did you ever find a fix? thanks in advance!

rtmag commented 5 years ago

I solved this issue by installing another newer version of gawk with: sudo apt-get install gawk

However, a different error, popd up. I'll raise a new issue...