Identify adapter position
Hi,
Is it possible to identify whether our specific adapters are 5' forward/reverse or 3' forward/reverse.
We are using Illumina Paired End data with the read length of 150*2. The protocol is TrueSeq mRNA stranded kit.
Thank you, Toufiq
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Any QC tools will tell you that. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Also you can extract some reads from your file and open them in a text editor, you'll see if your 5' or 3' are similar
In Illumina tech adapter sequences can only show up on 3'-end of your reads. You may also have adapter dimers but those will need to be completely removed.
If you have not seen it, there is a core sequence that is common for all indexed adapters, including TruSeq. Once this sequence is found generally everything to the right of that is removed by trimming program.
You will find the core sequence included in BBMap package in
resourcesdirectory. See this guide for more.To add: the TrueSeq mRNA stranded kit protocol also discusses the sequences of the adaptors if you need further details.