How to run BBMap and VCFtools for a 200 of WGS .fasta files in a for loop in Shell or Bash without printing file names??
How to run BBMap and VCFtools for a 200 of WGS .fasta files in a for loop in Shell or Bash without printing file names??
Have been advised to use that code for BBMap:
bbmap.sh ref=ref.fa (wait for that to finish) bbmap.sh in=reads1.fq out=mapped1.sam bbmap.sh in=reads2.fq out=mapped2.sam bbmap.sh in=reads3.fq out=mapped3.sam
This can`t be used for an automatic pipeline, cause requires file name writing. How to make that using for loop and without need to rewrite file`s names? Thanks.
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elvissober •
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Hello elvissober!
Questions similar to yours can already be found at:
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Cheers!
PS: In addition it's a question about for loops, nothing specific to bioinformatics.