adding segment data from CNAkit-RNA?

[ChristofferFlensburg]

Hi Eric!

Thanks for sharing your scripts, and a great method!

I am preparing a paper on CNA calling from RNA-Seq with superFreq and I want to compare to your results, but I struggle to get them. I have installed CNVkit, and I can run the top level Makefile in this repo (although with plenty of warnings), but the Makefile in the rna subdirectory immedaitely runs into an error:

make: *** No rule to make target /home/flensburg.c/code/cnvkit/scripts/cnv_expression_correlate.py', needed by tcga-skcm.cnv-expr-corr.tsv'. Stop.

I guess this is because CNVkit isn't installed where the script expects it to?

I can continue to chase that down, but it'd be easier for me if I can get the segmented calls from CNVkit directly, without having to run the Makefile. I see the TCGA data is already there. Would it be possible and easy for you to add the CNVkit RNA results to the repo as well?

Also, is there anything else I should think about when comparing to your method? Like, do you have any updates or something like that? I wanted to email you, but couldn't find your address at ucsf.edu. :/ Then I considered DMing on twitter instead, but opted for issue on github in the end! :D

Thanks again, and all the best,
/Christoffer

[etal]

Hey Christoffer, sorry for the delay. The cnvkit-examples repo is not as user-friendly as it could be. In particular, it looks like I've hard-coded the expectation that you have both the cnvkit-examples and cnvkit repos under $HOME/code/. I'll see about fixing the rough edges in that Makefile.

GitHub issues are easiest to keep track of, but DM is fine, too. My UCSF e-mail was inactivated since I left for DNAnexus this year.