Question: trimmomatic with paired-end
0
gravatar for j.m.fustin
5 months ago by
j.m.fustin10
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!

JM

ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 5 months ago by j.m.fustin10
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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: https://galaxyproject.org/learn/

Trimmomatic manual: http://www.usadellab.org/cms/index.php?page=trimmomatic

Thanks! Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k
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