How to find Adapter sequence for trimming

[Maryam_Momeni]

I am analyzing an RNA-seq dataset (GSE174302) produced using the HiSeq X Ten platform (GPL20795) for Homo sapiens. The fastQC report revealed failed Adapter Content checks, indicating that adapter sequences may be present in the reads. I would like to trim the adapter sequences but am unable to identify them.

The overrepresented sequences in the fastQC report show NO HIT

.I searched about HiSeq X Ten platform and I found that HiSeq X Reagent Kits support the TruSeq DNA PCR-Free Library Preparation Kit. Then I tried to find the adapter sequence in the Illumina adapter sequence sheet.

But, non of the adapters there were identical with the overrepresented sequences in the fastQC report.

Is there a Galaxy tool that gives me the adapter sequence or is there another way to do that?

[jennaj]

@Maryam_Momeni

But, non of the adapters there were identical with the overrepresented sequences in the fastQC report.

Maybe try with the closest match and see what happens?

This is a deprecated sequencing platform, so finding the information might be tricky but I can’t think off hand of a better solution other than checking the publication, and maybe contacting the GEO study author. GEO Accession viewer

I don’t know of a tool wrapped in Galaxy tool that will do more to check for and report “known” adaptors than FastQC, but if someone else does, they are certainly welcome to add more.

Hope this works out, and if you want to post back what worked, that will probably help someone else later on. Thanks!