How to use BBMap for aligning a set of .fastq files?

Question

[usgenome2018]

Want to run BBMap for a set of 30 .fastq files

Tried

#!/bin/bash
for n in {ls*.fastq}
do
  ./bbmap.sh "in=$n" "out={.}"
done

and (with GNU parallel)

ls *fastq | parallel ./bbmap.sh {} mapped_ {.}

What to change in code to make it align .fastq files against a preset reference?

Thx

[Sean Davis]

Can you not just add the reference file to the command line?

[usgenome2018]

reference has been preset

[User 59]

Preset where? How? What errors are you recieving?

[usgenome2018]

./bbmap.sh ref=ref.fa # creating index file from the input reference

problem is to input the in and out arguments of the bbmap.sh script in a bash for loop or in the parallell pipeline, errors are no arguments recognized correctly, thread exceptions, thank you

Answer 1

[Matt Shirley]

Take a look at Brian's comments here: How to do BBmap batch processing correctly?