Hi Guys,
I have Illumina NGS DNA 150 BP paired end reads.
My initial Fasqc report indicated the presence of Kmers towards the end of the reads at 145-147.
I used trimmomatic to trim them off. I trimmed 5 BP from the start of the read and 5 BP at the end of the read which makes my read length 140 bp (and should remove the kmers). However, when I looked at the Fastqc report post filtering, it showed that the kmers still exist but are now in the position 135-136. I have attached the pre and post filtering Fastqc reports if it helps to visualize them.
My trimmomatic trimming command was as follows:
java -Xmx15g -classpath trimmomatic-0.22.jar org.usadellab.trimmomatic.TrimmomaticPE -threads 4 -phred33 -trimlog trimmlog_log.txt input_R1.fastq input_R2.fastq output_R1.fq unpaired_output1.fq output_R2.fq unpaired_output2.fq HEADCROP:5 CROP:140 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:60
I would really appreciate it if any one can guide me through this issue as I couldn't figure it out.
I have Illumina NGS DNA 150 BP paired end reads.
My initial Fasqc report indicated the presence of Kmers towards the end of the reads at 145-147.
I used trimmomatic to trim them off. I trimmed 5 BP from the start of the read and 5 BP at the end of the read which makes my read length 140 bp (and should remove the kmers). However, when I looked at the Fastqc report post filtering, it showed that the kmers still exist but are now in the position 135-136. I have attached the pre and post filtering Fastqc reports if it helps to visualize them.
My trimmomatic trimming command was as follows:
java -Xmx15g -classpath trimmomatic-0.22.jar org.usadellab.trimmomatic.TrimmomaticPE -threads 4 -phred33 -trimlog trimmlog_log.txt input_R1.fastq input_R2.fastq output_R1.fq unpaired_output1.fq output_R2.fq unpaired_output2.fq HEADCROP:5 CROP:140 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:60
I would really appreciate it if any one can guide me through this issue as I couldn't figure it out.
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