Question: Bulk quality filtering with bbduk
gravatar for Felix_1993
2.2 years ago by
Felix_19930 wrote:


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 -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 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)

alignment sequence • 1.1k views
ADD COMMENTlink modified 2.2 years ago by genomax59k • written 2.2 years ago by Felix_19930

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.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by genomax59k
gravatar for genomax
2.2 years ago by
United States
genomax59k wrote:

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 -Xmx1g in1=$i\_read1.fq in2=$i\_read2 out1=$i\_clean_read1.fq out2=$i\_clean_read2 qtrim=rl trimq=10

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

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by genomax59k

Thanks! Worked like a charm!

ADD REPLYlink written 2.2 years ago by Felix_19930

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 -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 

I hope the loop is correct ..

ADD REPLYlink modified 8 months ago • written 8 months ago by krushnach80440
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1310 users visited in the last hour