Nextera pair end adapter cleaning

Question

[Rahul]

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.

Answer 1

[Jennifer Hillman Jackson]

Cross-posted: https://biostar.usegalaxy.org/p/29594/

[Rahul]

thank you very much for your comment. After using inbuilt nextera adapters, I got rid of all nextera adapters from lib. But still, it showing illumina universal adapters and solid small RNA adapters in lib. Can you please suggest me the possible trick to remove it. Thanks