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Old 04-17-2014, 10:28 PM   #1
Alex Lee
Junior Member
 
Location: N. Cal

Join Date: Apr 2014
Posts: 8
Talking 3' trimming using cutadapt changes property of 5'.

Hi all,
beginner question here: I have an attached PDF before and after illustration.

I'm using the Galaxy suite and cutadapt on a single read, not paired. When I first run the fastqc report, the kmer portion indicated that I might have a contamination in 3' end. I then used the cutadapt to trim and run the report over. Whereas it was about 90-100 at the 3' end now all k-mer at the 3' end are even around 40, however the first 1-5 (5' end) has shot up and now ranging from 80-100; question is why and what did I do wrong? Why would trimming the 3' end change the property of the 5'?
A bonus question is I heard that trimming on paired (forward+reverse) is better; does anyone know how to do this with Galaxy?

Thank you very much.

Alex
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File Type: pdf before_after.pdf (279.0 KB, 6 views)
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