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comparison htseq.pl @ 13:6324eefd9e91 draft default tip

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author fcaramia
date Tue, 16 Dec 2014 18:24:39 -0500
parents ebd59bc6855c
children
comparison
equal deleted inserted replaced
12:d49d06d35683 13:6324eefd9e91
54 # run htseq 54 # run htseq
55 my @htseq; 55 my @htseq;
56 my $COMM; 56 my $COMM;
57 my $file_type = `file $input_file`; 57 my $file_type = `file $input_file`;
58 if(grep /text$/, $file_type ) { 58 if(grep /text$/, $file_type ) {
59 $COMM = "htseq-count -q -m $OPTIONS{m} -s $OPTIONS{s} -a $OPTIONS{a} -t $OPTIONS{t} -i $OPTIONS{i} $input_file $OPTIONS{g}"; 59 $COMM = "htseq-count -r -q -m $OPTIONS{m} -s $OPTIONS{s} -a $OPTIONS{a} -t $OPTIONS{t} -i $OPTIONS{i} $input_file $OPTIONS{g}";
60 @htseq = `$COMM`; 60 @htseq = `$COMM`;
61 } else { 61 } else {
62 $COMM = "samtools view $input_file | htseq-count -q -m $OPTIONS{m} -s $OPTIONS{s} -a $OPTIONS{a} -t $OPTIONS{t} -i $OPTIONS{i} - $OPTIONS{g}"; 62 $COMM = "samtools view $input_file | htseq-count -r -q -m $OPTIONS{m} -s $OPTIONS{s} -a $OPTIONS{a} -t $OPTIONS{t} -i $OPTIONS{i} - $OPTIONS{g}";
63 @htseq = `$COMM`; 63 @htseq = `$COMM`;
64 } 64 }
65 65
66 my $row = 0; 66 my $row = 0;
67 $report{$sample} = "Command Used: $COMM\n"; 67 $report{$sample} = "Command Used: $COMM\n";