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novoalab / EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
GNU General Public License v2.0
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checking docs #25

Closed DrOllyGomez closed 4 years ago

DrOllyGomez commented 5 years ago

Hiya. I'm just going through the documentation, prior to installing and trying out, just to get straight what's needed, following through the pipeline. Can I just confirm that step 7 in the docs, instead of reading...

python2 slide_per_site_var.py mod.ref.per_site.var.csv > mod.per_site.var.sliding.win.csv python2 slide_per_site_var.py unm.ref.per_site.var.csv > unm.per_site.var.sliding.win.csv

..should actually read....

python2 slide_per_site_var.py mod.per_site.var.csv > mod.per_site.var.sliding.win.csv python2 slide_per_site_var.py unm..per_site.var.csv > unm.per_site.var.sliding.win.csv

I reckon so, otherwise I've missed something. many thanks

Huanle commented 4 years ago

Hi @DrOllyGomez , It seems it's a question about the naming of the input file, which is the output file of the last step. Right? You can feel free to name the file in your own style. BTW, I am going to release an updated version of epinano which will be slimmer. Thanks for using the pipeline.