fastq direction

Question

[gagi1993]

Hi,

I have one question if someone already did it so he can help. I have sequenced -ssrna virus with nebnext ultra directional 2 kit so that direction of cDNA is preserved with illumina 2x150bp. My question is so if i want to know if something is happening on genome (so -ssrna) or antigenome (it opposite) how to do it. My thought is to actually split r1 and r2 in 2 more fastqs that will have r1 that align to ref genome and its r2 counter part and opposite r1 align and it's r2 . I would do 2 separate stuff with those r1 and r2. I don't if this is right method. If someone already did something like this or knows how to do it your help would be very appreciated

Thanks

[GenoMax]

You may want to do this --> Single-end strand specific Rna-Seq: how to separate alignments by strand

[gagi1993]

thank you for the information a lot