Gmapper-Ls With Several Fastq Files

Question

[alan.lahure]

Hello everybody,

I would like to know if it's possible to put several reads (fastq) files with gmapper-ls (SHRiMP) ? I know it's possible to put the option -1 and -2 but I have a lot of fastq files.

Thank you

Answer 1

[Ashutosh Pandey]

I dont think so. You will have to run independent commands for each pair of fastq files.

Answer 2

[alan.lahure]

Thank you for your response. I'll manage.

Answer 3

[ramarquezo]

try with a loop "for file in" ...