Sequence Length Distribution after trimmomatic

Question

[marongiu.luigi]

Hello,

I have trimmed my sequences with TRIMMOMATIC using the following command:

trimmomatic.sh PE  -phred33 -threads 8 <seq_1.fq.gz> <seq_2.fq.gz> <seq_1_paired.fq.gz> <seq_1_unpaired.fq.gz> <seq_2_paired.fq.gz> <seq_2_unpaired.fq.gz>  LEADING:13 TRAILING:13 SLIDINGWINDOW:7:30 MINLEN:30

I think the trimming has been a good thing to do because the quality control (performed with FASTQC) shows slightly better sequences, with higher quality overall and lower warning flags. For instance, the original seq_1 has the following features:

The file also shows the presence of the adaptors, even if they do not show in the adapter content flag (maybe because Trueseq is not listed in the graph):

The trimmed sequence gives:

To note that both sequences have a GC and per tile warnings (nothing much I can do there, is it?), but the trimmed does not have the adapter and k-mer warnings anymore, along with higher per base quality.

HOWEVER, the trimmed sequence has the Sequence Length Distribution flagged. Can I simply ignore this flag, since I think is coming out simply from the fact that I reduced the reads' length?

Thank you.

Answer 1

[Sej Modha]

I think it is safe to ignore that especially if you have removed reads shorter than a certain length as part of the trimming and adaptor cleaning.

[Devon Ryan]

I've moved this to an answer, since it's absolutely correct.