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MonashBioinformaticsPlatform / RSeQC

fork of RSeQC python RNAseq metrics suit of tools
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geneBodyCoverage for 100+ libaries #3

Open gnmcsbnfrmtcsclb opened 4 years ago

gnmcsbnfrmtcsclb commented 4 years ago

Greetings!

Since out experiment contains 100+ libraries, the gene body coverage line plot and heatmap plot are unable to display all the names. We've also run gene body coverage on the individual input BAM files.

We realize that it is possible to take the *.txt output from individual input runs and convert them to line plots and heatmaps, but since we are new to R, we had to put in some time to get that done. So as undergrad newbies to R, and NGS, may we request some additional feaures to your RSeQC as optional flags while runnin geneBodyCoverage:)

A. suppress the input names altogether B. shorten names to contain just the unique part of it as the basename B. change margins C. in line plot only mention names of inputs with the x% most deviation from the rest (x = user defined) D. ensure plotting and legend listing are based on natural rather than the default alphabetical sort

Thanks, in advance. Lotte

serine commented 4 years ago

hey @gnmcsbnfrmtcsclb not sure if you realised but this isn't official repository for RSeQC. I "forked" a while back for my own needs but never really did much with it. Original site is here http://rseqc.sourceforge.net/ I don't think there an official RSeQC github account, and this is why you don't see your typical github fork connection.

So I won't be able to help, perhaps try contacting RSeQC via email..?

All the best