Question: trimmomatic with paired-end
gravatar for j.m.fustin
8 months ago by
j.m.fustin10 wrote:

Dear Biostar,

I have paired-end sequencing data I would like to trim using trimmomatic. I have read 1 which matches the antisense sequence of the input and read 2 which is the sense paired-end read. I confirmed the presence of illumina adapter by fastQC. Can I simply use the provided Truseq3 (paired-end for mi-seq and Hi-seq) as adapter sequence to trim? I wonder whether I will have a problem with the antisense read?

Thanks in advance!


ADD COMMENTlink modified 8 months ago by Jennifer Hillman Jackson25k • written 8 months ago by j.m.fustin10
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Trimmomatic works with strand-specific reads. Run the data through Trimmomatic, then run FastQC again, and compare to the original report to review how clipping modified the data.

Galaxy tutorials:

Trimmomatic manual:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 8 months ago by Jennifer Hillman Jackson25k
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