Question: Sequence Length Distribution after trimmomatic
0
gravatar for marongiu.luigi
17 months ago by
Germany, Mannheim, UMM
marongiu.luigi420 wrote:

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:

enter image description here enter image description here enter image descripthe tion here 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):

enter image description here enter image description here

The trimmed sequence gives:

enter image description here enter image description here enter image description here

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.

sequence next-gen • 1.4k views
ADD COMMENTlink modified 17 months ago • written 17 months ago by marongiu.luigi420
1
gravatar for Sej Modha
17 months ago by
Sej Modha4.5k
Glasgow, UK
Sej Modha4.5k wrote:

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.

ADD COMMENTlink written 17 months ago by Sej Modha4.5k
1

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

ADD REPLYlink written 17 months ago by Devon Ryan92k
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