fastq format foward only or interleaved fastq?

[jianshu93]

Dear author,

I want to ask what is the default fastq file, only foward reads or reverse reads or interleaved reads?

Thanks,

Jianshu

[loic-couderc]

Dear @jianshu93,

You can either interleave your paired-end reads, or just concatenate the forward and reverse files in a single file. However MATAM will treats this reads as single reads and will not fully benefits of paired-end reads (they will just be considered as single reads).

cheers