Closed vreuter closed 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.
:+1: thanks @afrendeiro
Cloned the relevant repo and got the script, thanks again!
I tried subbing in the script from
pipelines/tools
that sounds like it could've been a substitute for thespp
tool referenced in the pipeline config file'stools
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 likerun_spp.R
andspp_peak_calling.R
are for different things?