Prior to alignment of RNA-seq data

Question

[sarah.laverty20]

Hi there!

I am working through RNA-Seq data for the first time. I have run FastQC on all my samples and nothing abnormal is being flagged, I am therefore assuming I do not need to trim any of my sequences, is this correct and am I able to move on to alignment now or is there anything else I should do prior to alignment?

Thanks!

Answer 1

[dsull]

correct, go ahead and align! Go ahead with kallisto/salmon/STAR/Hisat2 or whatever you plan on using.

[sarah.laverty20]

Thank you!

Answer 2

[GenoMax]

If you are simply going to align to a good existing reference then you can move forward with alignments. Aligners will soft-clip any bases that do not map, which will take care of any residual adapter or other sequences. If you intend to do any de novo assembly work then you should trim your data. There may be no contamination present but you want to be certain there is none for that type of work.