Dear great helpers,
I'm an RNAseq starter and trying to find a good tool for fastq file preprocessing. I currently use BBmap to trim Illumina addapter using the command:
bbduk.sh -Xmx1g in1=f1.fq in2=f2.fq out1=clean1.fq out2=clean2.fq ktrim=r ref=truseq_rna.fa.gz k=28 mink=12 hdist=1
The f1.fq and f2.fq are from Illumina 1.9. When I check the output clean1.fq and clean2.fq files using FastQC. There is still evidence of adapter contamination.
GATCGGAAGAGCACACGTC 25845 0.18387555456141572 Illumina Multiplexing Adapter 1 (100% over 19bp)
I think this could be solved by adjusting parameters, but I'm too naive to do it. Would you please suggest me how to solve the problem?
Thank you very much in advance,
Kaj
I'm an RNAseq starter and trying to find a good tool for fastq file preprocessing. I currently use BBmap to trim Illumina addapter using the command:
bbduk.sh -Xmx1g in1=f1.fq in2=f2.fq out1=clean1.fq out2=clean2.fq ktrim=r ref=truseq_rna.fa.gz k=28 mink=12 hdist=1
The f1.fq and f2.fq are from Illumina 1.9. When I check the output clean1.fq and clean2.fq files using FastQC. There is still evidence of adapter contamination.
GATCGGAAGAGCACACGTC 25845 0.18387555456141572 Illumina Multiplexing Adapter 1 (100% over 19bp)
I think this could be solved by adjusting parameters, but I'm too naive to do it. Would you please suggest me how to solve the problem?
Thank you very much in advance,
Kaj
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