BBDuk quality filtering not producing expected results
I’m trying to trim/filter low quality reads from paired-end exome-seq data, using BBDuk.
I used the command:
for ea in $files; do R1="$ea" R2=$(echo $R1 | sed "s/R1/R2/") /home/shared/programs/bbmap/bbduk.sh -Xmx1g in1=$R1 in2=$R2 out1="$(echo $ea | sed s/.fastq.gz/_trimmed_filtered.fastq.gz/)" out2="$(echo $(echo $ea | sed s/R1/R2/) | sed s/.fastq.gz/_trimmed_filtered.fastq.gz/)" ref=/home/shared/programs/bbmap/resources/adapters.fa t=10 ktrim=r k=23 kmin=11 hdist=1 maq=10 minlen=60 tpe tbo done;
After running fastqc on the output of this, I’m seeing that R2 files have some reads with low quality scores (see per sequence quality score), and the overrepresented sequence “NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN”, which should have been filtered out by quality filtering, no?
Any help here would be much appreciated.
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