I was not able to get this working but i found my answer here https://unix.stackexchange.com/questions/429502/how-to-input-multiple-files-from-a-list-of-files-in-bash-script/429506?noredirect=1#comment775512_429506
thanks
How to input multiple files from a list of files
I have a list of files in bam_files.txt which looks like this
less bam_files.txt
/home/test/2cells_2_trim.bam
/home/test/6h_1_trim.bam
/home/test/2cells_1_trim.bam
/home/test/6h_2_trim.bam
I want to do something like this
cuffnorm -o cuffnorm_out /home/software/genes.gtf test/*.bam
but while reading files from bam_files.txt and not directly from directory (as shown above).
Can someone please help. Thanks a lot. Appreciate your help.
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Alex Reynolds
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Goku •
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Goku •
1 answer
Perhaps a bash process substitution will help:
$ cuffnorm ... <(cat bam_files.txt | tr '\n' ' ')
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