Explanation for kmer enrichment after skewer trimming of the RNA-seq reads

Question

[tobytaogf]

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?

[GenoMax]

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Answer 1

[hongshan.jiang]

In your case, there is NO need to specify -m or -l option!

Adapter: -m, --mode <str> trimming mode; for paired-end files -- pe: paired-end; mp: mate-pair; ap: amplicon (DEFAULT: pe) Filtering: -l, --min <int> The minimum read length allowed after trimming; (DEFAULT: 18)

Please try the following command instead: skewer-master/skewer Phragmites_RNA/raw_data/PL_R1.fastq Phragmites_RNA/raw_data/PL_R2.fastq -o Phragmites_RNA/raw_data/skewer/PL