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
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