I would like to know if I can pass a fastq file in trimmomatic, and then pass again its results. Also, how can I be sure that a fastq file that I downloaded from public sources has already been trimmed for quality?
I got some SRA fastq files that seems that they have already been trimmed, since their reads are not the same lengh. But when i look at them in the Fastqc, it redflags a significant number of reports (as for example GC contents and overrepresented sequences). When I pass it again in trimmomatic, some of the reports in Fastqc get a better. So my doubt is if it's ok to do this, pass them twice in the trimmomatic. In the comments are some examples of what I got.
Thanks
1 answer
If it is Illumina data and the reads are not the same lengths then it has been trimmed.
You can pass files as many times as you want, now what happens is not always obvious, normally one would expect that nothing will change second times around, but in reality, algorithms may work in unexpected ways, have various initial conditions, thus the second time you might still get changes (I don't how Trimmomatic works here, I am just pointing out that it could happen even if seems counterintuitive)
Log in to answer this question.
-
Sequence Duplication for Single-End 3RAD Data
written by Sarah •
-
Fastp Trimming for WGS
written by j.k3096 •
-
How to interpret that overrepresented and duplicate sequences influence %GC content?
written by tvibhaps •
-
Why does Phred+ encoding changes after trimming fastq files??
written by Bikal •
-
Help with the reads filtering process
written by valentinavan •
-
Server denied on SRA download
written by vitor •
-
Per sequence GC content still not good after trimming
written by zouini6 •
-
kmer content changes after trimming and removing adapters from reads
written by serpalma.v •
-
How to repair *all* problems identified by FastQC?
written by dec986
-
GC content and Kmer
written by Xin
it can be done. But it would help us understand if you could tell us why two pass is necessary for your work.
The thing is that I got some SRA fastq files that seems that they have already been trimmed, since their reads are not the same lengh. But when i look at them in the Fastqc, it redflags a significant number of reports (as for example GC contents and overrepresented sequences). When I pass it again in trimmomatic, some of the reports in Fastqc get a better. So my doubt is if it's ok to do this, pass them twice in the trimmomatic. Here goes some images that explain what I got. (The Filename is after passing is with a 6 in the place of 5, It was a typo)
There are no restrictions on number of times in filtering reads.