search

honzee / RNAseqCNV

R package for large-scale CNV analysis from RNA-seq
MIT License
11 stars 8 forks source link

Format for gene level counts #20

Closed anashank closed 1 year ago

anashank commented 1 year ago

Hi, I was wondering if it would be possible to use the output from tools like Salmon, which has a different method of counting reads compared to tools like HTSeq?

honzee commented 1 year ago

Hi,

thanks for the question! We have yet to test running RNAseqCNV with output count files from salmon. However, I think as input, it should work very similarly to HTSeq. Just make sure, that the count files are in the format specified in README.

Best, Jan

anashank commented 1 year ago

Thank you!