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