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Old 07-07-2014, 02:43 PM   #1
Alex Lee
Junior Member
Location: N. Cal

Join Date: Apr 2014
Posts: 10
Smile Kmer changes after Trimming

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.
Attached Files
File Type: pdf before_trimm.pdf (328.2 KB, 44 views)
File Type: pdf after_trimm.pdf (393.7 KB, 11 views)
File Type: pdf all.fa.pdf (89.3 KB, 5 views)
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Old 07-07-2014, 03:29 PM   #2
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Location: UK

Join Date: Jan 2010
Posts: 390

This really needs to be a FAQ item on here:
Bukowski is offline   Reply With Quote

rna sequencing, trim adapter, trimming, trimmomatic

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