Question: Explanation for kmer enrichment after skewer trimming of the RNA-seq reads
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gravatar for tobytaogf
5 weeks ago by
tobytaogf0
tobytaogf0 wrote:

Hi. I have some Phragmites RNA seq data. I tried to use Skewer to trim the adapter of these reads, as the code " skewer-master/skewer -m pe -l 50 Phragmites_RNA/raw_data/PL_R1.fastq Phragmites_RNA/raw_data/PL_R2.fastq -o Phragmites_RNA/raw_data/skewer/PL" After trimming, I run fastqc of these trimmed data to check the qualities. I found all these data have the kmer flag and position either on the front or the end position. However, the adaptor section did not give me the flag. I am wondering what cause these kmer issues and do I need to worry these for my downstream analysis. Or parameter setting of the skewer is wrong?

PL_R1 PM_R1 PL_R2

fastqc kmer skewer • 100 views
ADD COMMENTlink modified 5 weeks ago by genomax64k • written 5 weeks ago by tobytaogf0

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