Discard the reverse reads

[shashankgpt]

Hi,
We have done the sequencing (2*250bp) for the V3-V4 region (341f-806r). The quality of reverse reads is very bad, and if I truncate the bad quality reads from the reverse reads, I may not get the decent overall while merging, hence loose many reads.

I was just wondering, what if I discard my reverse reads for downstream analysis. What are the advantages or disadvantages of doing this? I guess one of the advantages of using forward reads is that I may lose so many reads because in my case, I won't merge the forward and reverse reads. Secondly, how this affects the taxonomy classification?
Best

[Mehrbod_Estaki]

Hi @shashankgpt,
2x250bp for V3-V4 region is rarely a good idea in my experience as the reason you mentioned they often fail to merge. 2x300 should be sufficient however for your future considerations. As for your original question, I think using the forward reads is your best option and the loss in taxonomic resolution is not that detrimental at all. This event occurs often enough!