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Old 10-13-2021, 08:57 AM   #1
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Location: USA

Join Date: May 2021
Posts: 7
Default BBDuk quality filtering not producing expected result

I'm trying to trim/filter low quality reads from paired-end exome-seq data, using BBDuk.

I used the command:

for ea in $files;
R2=$(echo $R1 | sed "s/R1/R2/")
/home/shared/programs/bbmap/ -Xmx1g in1=$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

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".

Looking at these reads in the fastq:
@HISEQ:525:HMFYNBCXX:1:1101:1380:2167 2:N:0:CAGATC
@HISEQ:525:HMFYNBCXX:1:1101:1276:2219 2:N:0:CAGATC
@HISEQ:525:HMFYNBCXX:1:1101:1238:2328 2:N:0:CAGATC

Shouldn't these reads have been filtered out?

Any help here would be much appreciated.

Last edited by reliscu; 10-13-2021 at 09:15 AM.
reliscu is offline   Reply With Quote

bbduk, exome sequencing, filtering reads

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