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rr1859 / R.4Cker

MIT License
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bed files are not sorted #22

Open geneticoman opened 7 years ago

geneticoman commented 7 years ago

Hi,

I noticed that the *unique_2.bed files generated with the reduced_genome.sh script are not sorted correctly (by chromosome and then start position), this breaks the step where you remove the self-ligated and undigested fragments where you find the sequence before and after the bait. You should include a sorting step in your script.

rr1859 commented 7 years ago

Hi,

Line 28 of the reduced_genome.sh does sort the file by chr and start position before getting the unique lines. Did you have any other trouble running the script?

geneticoman commented 7 years ago

Hi,

You are right! It looks like I was using an older version of your script since I noticed that you updated that particular line on Aug 18, 2016. I checked and in our script it just says sort not sort -k1,1 -k2,2n. I think I might have to update your code and rerun the analysis because we were getting some errors as well with nearbait, cis, and trans. For trans analysis, I believe however I was using a more recent version of the code installed in my laptop and for some of my samples it gave a warning that it couldn't solve the Hessian and that only 1 iteration was done.