reduced quality of lane 4 compared to other lanes (paired-end Illumina)

Question

[rosies]

Hi there,

I have paired end Illumina (NextSeq) data (Staph aureus, avg sequence length 150bp). After running FastQC, I found reads from Lane 4 R2 to have reduced quality compared to that in Lane 1-3, R1 and R2. With most Lane 4, R2 from my samples (100+ samples) I would need to trim 30 bps whereas I wouldn't need to trim more than 5 bps from the other lanes. Should I just discard the data from this lane? or trim the reads from Lane 4 R2 (and some R1) separately before concatenating the forward (and reverse).

Thank you.

[glihm]

Hi rosies,

did you multiplex your samples ? I mean, in the lane4, what do you have ? Only one sample ? One condition ? Or all conditions multiplexed as in lanes 1-3?

Theses details will help us to answer you better. :)

[Juke34]

I have seen same problem with lane3+lane4. Aberrant increase of error rate