How to trim bases with bbduk.sh

Question

[shivangi.agarwal800]

Hi,

I am using BBMAP following command to trim adapter sequences from the fastq files.

bbduk.sh -Xmx1g \
  in1=1_R1_001.fastq.gz \
  in2=1_R2_001.fastq.gz \
  out1=1_R1_001-trimmed.fastq.gz \
  out2=1_R2_001-trimmed.fastq.gz \
  literal=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
  qtrim=rl \
  trimq=20 \
  ktrim=r \
  k=16 \
  filterpolyg=5 \
  tbo tpe

Can anyone let me know how can I use bbduk to trim the first 5 bases from the demultiplexed FASTQ files?

Thanks

Answer 1

[GenoMax]

from the demultiplexed FASTQ files?

You can use forcetrimleft=4 to remove the first 5 bases. Do you want to do this before the operation above or later? You can do this via a pipe.