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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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Nucleotide level mismatch information with Epinano_Variants.py #141

Closed kaltinel closed 1 year ago

kaltinel commented 1 year ago

Hi,

I hope you are well.

I am kindly writing to you to learn, whether there is a way to extract the mismatched nucleotide frequency information out of Epinano_Variants.pyoutput. This would be the information of mismatch frequencies, not cumulative for all nucleotides, but per nucleotide, such as:

#Ref,pos,base,strand,cov,q_mean,q_median,q_std,mis_A,mis_C,mis_G,mis_T,ins,del
chr1,7,G,+,6644,20.81644,22.00000,5.89298,0.00135,0.002,0.0025,0.0005,0.00602,0.00045

Looking forward to hearing from your side, thanks!

enovoa commented 1 year ago

Hi @kaltinel i believe that what you are looking for is EpiNano_RMS.py, which is available in the nanoRMS repository. The usage of this script is explained in the README. Best, Eva