Bulk quality filtering with bbduk

Question

[Felix_1993]

Hi,

I sequenced some gut-samples for microbial communities (16S, paired-end, Illumina MiSeq, fastq).

e.g. Sample1_read1.fq Sample1_read2.fq Sample2_read1.fq Sample2_read2.fq ...etc

I am following the Mothur SOP, however, due to the partially bad read quality, I incorporated a quality filtering step before aligning the reads. Therefore, I use a tool from the BBDuk package

bbduk.sh -Xmx1g in1=Sample1_read1.fq in2=Sample1_read2 out1=Sample1_clean_read1.fq out2=Sample1_clean_read2 qtrim=rl trimq=10

Everything works fine, but now I'd like to run everything in one batch. How can I create a loop so the bbduk.sh goes through all the files in my folder (and always takes read1 and read2 of the same sample)?

Thanks a lot for your help in advance! (And let me know if I missed some vital information)

[GenoMax]

Use these for inspiration: A: bash loop for alignment RNA-seq data or A: shell script for bowtie/bwa alignment pair end reads

Post if you would like additional help.

Answer 1

[GenoMax]

There can be many variations of this (and each one would get the job done).

for i in `ls -1 *_read1.fq | sed 's/_read1.fq//'`
do
bbduk.sh -Xmx1g in1=$i\_read1.fq in2=$i\_read2 out1=$i\_clean_read1.fq out2=$i\_clean_read2 qtrim=rl trimq=10
done

If you are using a job scheduler on a cluster wrap necessary bits around the bbduk command to submit individual jobs to scheduler.

[Felix_1993]

Thanks! Worked like a charm!

[1769mkc]

my files are as such

SRR2753090_1.fastq   SRR2753090_2.fastq

managed to do it..

just for my clarification this is what im using

for i in `ls -1 *_1.fastq | sed 's/_1.fastq//'`
do
bbduk.sh -Xmx1g in1=$i\_1.fastq in2=$i\_2.fastq out1=$i\_clean_1.fastq out2=$i\_clean_2.fastq ref=/src/bbmap/resources/adapters.fa 
done

I hope the loop is correct ..