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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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Is it possible to pass multiple features to Epinano_DiffErr ? #122

Closed katsikora closed 2 years ago

katsikora commented 2 years ago

Dear Team,

thank you for providing this innovative tool.

I'm currently testing Epinano_DiffErr on the output of Epinano_sumErr run on 5-mers. My file contains columns named #Ref,pos,base,strand,cov,sum_err1,sum_err2,sum_err3,sum_err4,sum_err5 . Is it possible to pass all the five sum_err columns to DiffErr? I tried with a comma-separated list and this failed.

Would you have a suggestion of what would be the best way to go about it?

I'm using Epinano 1.2.0.

Best regards,

Katarzyna

Huanle commented 2 years ago

Hi @katsikora ,

Unfortunately, Epinano_DiffErr.R is designed to handle a single feature at one time. So you will have to run it repeatedly for multi-features or once for combined features. But i will think about enabling it to handle multiple features.

Kind reminder: this script was made to analyze small RNAs. If you want to apply it to genome or very long transcripts, you'd better use it in a sliding window mode. Hope this helps.

Best, Huanle