gravatar for kuilin

2 hours ago by

Hi all, I have encounter some problem while trying to trim with cutadapt.

After trimming of the adaptor sequence and running fastqc, I got a warning for overrepresenting sequences:

Sequence:
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

Count: 55673

Percentage: 0.12298334311639213

I then do another round of cutadapt to remove the "G"s and I got an overrepresenting sequences that shows up empty,
with count of 88854, and percentage of 0.19600626265311266.

Then, I tried trimming the original sequence again with trimgalore, and basically got the same overrepresenting sequence warning as the first cutadapt attempt, showing many "G"s.

My question is, what have I done wrongly with the cutadapt? And whether I should trust the results from trimgalore?

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modified 2 hours ago

by

GenoMax96k

written
2 hours ago
by

kuilin0



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