#!/usr/bin/perl -w 

$dir = "demultiplexed_trimmed";

@files = qw(2AB_1_BC1.fastq  2AB_T_BC3.fastq  45a_1_BC4.fastq  91a_1_BC7.fastq  91b_1_BC9.fastq
2AB_2_BC2.fastq  45_2_BC5.fastq   45b_1_BC6.fastq  91a_2_BC8.fastq  91b_2_BC10.fastq);






foreach $f (@files){

#system("/home/common/hisat2-2.1.0/hisat2 --no-mixed --max-intronlen 10000  -x /home/common/hisat2-2.1.0/indexes/sc3/genome  -U $dir/$f -S $f.sam  ");
print "$dir $f \n";
system("/home/common/hisat2-2.1.0/hisat2 --qc-filter --no-mixed --max-intronlen 200  -x ./indexes/splrep -U $dir/$f -S sr_$f.sam  ");
print "##########################################\n";

}