Sequence Length Distribution after trimmomatic
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1
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3.5 years ago

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.

next-gen sequence • 4.4k views
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2
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3.5 years ago
Sej Modha 5.0k

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.

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

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