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@lpantano
Created February 5, 2015 15:51
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difference on code to get working in our reads.
2,3c2
< use lib '/scratch/lpantano/montreal/qc';
< use IO::Uncompress::Gunzip qw($GunzipError);
---
> use lib '/home/lpantano/soft/QC';
236c235
< $INSTREAM = IO::Uncompress::Gunzip->new("$infile1") or die "Couldn't open $infile1\n";
---
> open (INSTREAM, "$infile1") or die "Couldn't open $infile1\n";
239c238
< while ($current_line = <$INSTREAM>) {
---
> while ($current_line = <INSTREAM>) {
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< $current_line =~ s/:/_/;
< $current_line =~ s/:/_/;
254c251
< close $INSTREAM;
---
> close INSTREAM;
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< #open (INSTREAM, "$infile2") or die "Couldn't open $infile2\n";
< $INSTREAM = IO::Uncompress::Gunzip->new("$infile2") or die "Couldn't open $infile2\n";
---
> open (INSTREAM, "$infile2") or die "Couldn't open $infile2\n";
261c257
< while ($current_line = <$INSTREAM>) {
---
> while ($current_line = <INSTREAM>) {
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< $current_line =~ s/:/_/;
< $current_line =~ s/:/_/;
276c270
< close $INSTREAM;
---
> close INSTREAM;
280c274
< system ("bwa mem $ref -t 8 -c 1 Read1.fq Read2.fq >phix.sam");
---
> system ("bwa mem $ref -c 1 Read1.fq Read2.fq >phix.sam");
438,440c432
< @s=split(/\t/, $current_line);
< if ($s[5]=~/^\d+M$/) {
< #if ($current_line=~/80M/) {
---
> if ($current_line=~/80M/) {
467,469c459
< @s=split(/\t/, $current_line);
< if ($s[5]=~/^\d+M$/) {
< #if ($current_line=~/80M/) {
---
> if ($current_line=~/80M/) {
529,531c519
< @s=split(/\t/, $current_line);
< if ($s[5]=~/^\d+M$/) {
< #if ($current_line=~/80M/) {
---
> if ($current_line=~/80M/) {
558,559c546
< @s=split(/\t/, $current_line);
< if ($s[5]=~/^\d+M$/) {
---
> if ($current_line=~/80M/) {
@NS500227:6:H160HBGXX:1:11101:12956:1048 1:N:0:1
AGTCANCACGCCCAGCCTAATCCTGAGATCTTGTAANACATCTGGNGAGCCAGGTGGCNTNACCNNTG
+
AAAA.#F<FFFFFAFFFAFAFFFFF<FFFAFFFFA.#FF<FFFFF#F<FF<FFF<FFF#F#FFF##F.
@NS500227:6:H160HBGXX:1:11101:21174:1048 1:N:0:1
TAACCNTCTTAACAGCCCTNGGACGGAGGAGTTACGNGTTTATCANCTCGGCTCTAAGNTNCAGNNA
+
@NS500227_6_H160HBGXX:1:11108:2429:1048 1:N:0:1
AAAACNAAAAATGAGNTTAAATAACTANTNATATGNNTGTTATTTNCTGTNACTANNANANCTG
+
AA7AA#FF.FFF7FF#FFFF7FF<FAA#F#AFAFF##FF<<FA.F#7FF.#.F)<##<#.#FAF
@NS500227_6_H160HBGXX:1:11108:1920:1048 1:N:0:1
GAAGANGGTTCTGAGNATGCTTCTGATNTNGATCTNNGCGGTTTANCCCGNTAACNNCN
+
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