reduced quality of lane 4 compared to other lanes (paired-end Illumina)
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.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
problem with 16S reverse reads with low quality
written by michele.lamprillo •
-
PolyA in FastQC results from EM-Seq?
written by Watermelon •
-
Read groups for multi-lane sample
written by shivangi.agarwal800
-
Trimming Nextera adapter from scRNA paired reads with different length
written by almogangel •
-
Trimming Illumina universal adapters using cutadapt proving insufficient
written by jleehan •
-
Help Understanding PairedEnd read merging
written by m.radz •
-
De novo transcriptome assembly using Trinity
written by 1234anjalianjali1234 •
-
reduced quality in a paired-end R2 reads
written by Assa Yeroslaviz
-
Processing Metagenomics Reads from Multiple Lanes
written by adityabandla •
-
One sample pooled in a whole lane vs multiple sample in each lane
written by bob •
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. :)
I have seen same problem with lane3+lane4. Aberrant increase of error rate