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#Rename the #fasta #header and #keep first $ perl -ne 'if (/^(>\S+)/){print "$1\n";}else{print $_;}' realTestDATA.fa > realTestDATA_headerCorrected.fa #Perl

Store all files in a array using perl: my @filesbwa = <$base_name/reads/$base_name.$library.bwa.*fa> #Store #Keep #Array #Perl