MUFFIN regexp to detect reads in directory

[rhysnewell]

Hello,

I'm just wondering if there is a way to change the regexp that is used to detect short reads in the input directory? Currently it is *_R{1,2}.fastq{,.gz} and I need to set it to be *_{1,2}.fastq{,.gz} or something similar as reads from the SRA often don't have the R{1,2} in their filename. Additionally, sometimes reads are denoted with fq rather than fastq

I couldn't see a parameter to set these regexp or anything in the documentation but I may be blind. This seems like something people would regularly come across and need to change, rather than changing the names of their files to suit your regexp. Any help would be appreciated!

Cheers, Rhys

[rhysnewell]

Also, does MUFFIN support interleaved reads?