Question: Illumina Adapters for Small RNA seq
gravatar for russell.stewart.j
2.8 years ago by
russell.stewart.j0 wrote:


I'm quite new to bioinformatics. I'm attempting to trim adapters from an Illumina HiSeq 2500 dataset, prepped with a TruSeq prep-kit... however I can't figure out what the adapters are. First I extracted subsets of the data and ran alignments and consulted the illumina adapter document to try to figure it out:

The alignments make the size of the adapter look variable, but present in only about 90% of the data. So I consulted the internet which told me to run a fastQC and find overreppresented sequences (in a sample of 100,000 raw reads):

Which seems to return a lot of different adapters. I realize that this is actually quite simple, I just do not have the experience to know exactly what to trim. Using a NGS toolbox for small RNA processing, I can remove both 5' and/or 3' adapters if I know the sequence (or where it starts for 3'). Running this code on one of my datasets reduced it to 82%:

Any advice would be appreciated!

rna-seq • 2.5k views
ADD COMMENTlink written 2.8 years ago by russell.stewart.j0

Take a look at this thread: small RNA-seq pipelines

BBMap mentioned in the thread comes with a comprehensive adapters.fa file in the "resources" directory that covers all common illumina kits.

ADD REPLYlink written 2.8 years ago by genomax65k

Thanks for the reply. I do have the Illumina lists. I guess what I'm struggling with is how to decide what to trim, because when I tried to trim what I thought was the correct primer, it wasn't present in ~18% of my sequences.

ADD REPLYlink written 2.8 years ago by russell.stewart.j0

You could try sRNAWorkbench, it has some predefined illumina trueseq adapters for smallrna. Generally smRNA analysis requires only single end data, 3' adapter removal should be fine

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Prasad1.5k
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