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-   -   Kmer changes after Trimming (http://seqanswers.com/forums/showthread.php?t=44770)

Alex Lee 07-07-2014 01:43 PM

Kmer changes after Trimming
 
3 Attachment(s)
Hi All,
I'm getting higher Kmers on my 5' end after trimming with trimmomatic-0.32. My samples are paired RNA-Seq from Illumina Miseq. I'm using FastQC Report to detect overrepresentation of Kmers. My original untrimmed samples show a high overrepresentation of Kmers on my 3í end but after trimming its now on the opposite side. The command that I used is the following.

java -jar trimmomatic-0.32.jar PE -phred33 -trimlog log.txt F.fastq R.fastq f_m.fastq f_um.fastq r_m.fastq r_um.fastq ILLUMINACLIP:all.fa.fa:2:30:5:2:true LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36 TOPHRED33

Iím using a custom adapter file called all.fa. I made 3 pdf to show before, after and the custom adapter files. Iím doing something wrong but can't figure out what. Thanks in advance. ;)

Bukowski 07-07-2014 02:29 PM

This really needs to be a FAQ item on here:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896536/


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