Question: Nextera pair end adapter cleaning
0
gravatar for rahul.sg98
5 weeks ago by
rahul.sg980
rahul.sg980 wrote:

Can I use Nextera pair end adapter option in Galaxy Trimmomatic program for cleaning my illumina Nextera 500 transcriptome reads? or else I have to use Netera 500 adapter for cleaning lib.

assembly galaxy rna-seq • 156 views
ADD COMMENTlink modified 5 weeks ago by Jennifer Hillman Jackson25k • written 5 weeks ago by rahul.sg980
2
gravatar for Jennifer Hillman Jackson
5 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

From what you state, using Trimmomatic in Galaxy should be ok with the "Nextera (paired-ended)" built-in adaptors. But you can test it out and use customize adaptors (if needed) using the same tool form.

Run FastQC on the data before and after to review the trimming results (test to see if the adaptor was actually clipped correctly).

The functions in the Galaxy wrapper mirror those in the command-line version of Trimmomatic. Their manual covers usage/formatting that applies to both. See the section "The Adapter Fasta" here http://www.usadellab.org/cms/?page=trimmomatic

Thanks! Jen, Galaxy team

ADD COMMENTlink written 5 weeks ago by Jennifer Hillman Jackson25k
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