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epigen / open_pipelines

Pipelines for NGS data preprocessing by the Bock lab and friends
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Missing run_spp.R for chipseq.py #5

Closed vreuter closed 7 years ago

vreuter commented 7 years ago

I tried subbing in the script from pipelines/tools that sounds like it could've been a substitute for the spp tool referenced in the pipeline config file's tools section, but when I look at the sample's log file, it seems like the command being run would be appropriate for a different script, so it seems like run_spp.R and spp_peak_calling.R are for different things?

afrendeiro commented 7 years ago

They are indeed different (but related) things.

run_spp.R is from here. An ENCODE R library which has some programs which are not really packaged into installable command line tools but exist as a script. run_spp.R is (optionally) used by the ATAC/ChIP-seq pipelines to compute the NSC and RSC metrics.

tools/spp_peak_calling.R is a script I wrote that uses that spp library to call peaks and can be used by the two pipelines above is specified in the config file. I don't usually use spp for peak calling though and therefore haven't used that script in a long time.

vreuter commented 7 years ago

:+1: thanks @afrendeiro

vreuter commented 7 years ago

Cloned the relevant repo and got the script, thanks again!