Weird over-represented sequence in sn/scRNASeq fastqc
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22 months ago
Tania ▴ 180

Dear Fellows

I have a a weird over-represented sequences in my sn/scRNASe samples founs in fastqc report as in the photo attached. I doubt that these sequences are the source of getting ambient RNA warning? Any idea how to remove them? thank you

enter image description here

single cell nuclei FASTQC RNASeq • 593 views
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You could simply remove them by providing the core sequence (which seems to be about first half of the sequence above) to any trimming program.

That said, perhaps they are part of the kit you used. There may be specific instructions on how to process the data which would account for them.

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Thanks GenoMax. I will try to trim them, I can't find those specific instructions though? Thanks

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