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Thread | Thread Starter | Forum | Replies | Last Post |
Plasma DNA Puzzle | whw | Sample Prep / Library Generation | 9 | 08-03-2011 11:41 AM |
BWA puzzle: Read fate is not deterministic? | bhootnaath | Bioinformatics | 2 | 06-09-2011 12:50 PM |
blast puzzle | anyone1985 | Bioinformatics | 1 | 09-06-2009 02:45 AM |
format puzzle | anyone1985 | Illumina/Solexa | 0 | 03-13-2009 04:29 AM |
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#1 |
Member
Location: beijing Join Date: Jul 2008
Posts: 35
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hi, when I use fq_all2std.pl in MAQ to convert prb and seq files into a fastq file, i do not understand this line " if (($_&0x3) == 3)" in the follow script.
since the prb file is just like this " -40 -40 40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 -40 40 -40 40 -40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 40 -40 -40 -40 -40 -40 40 -40 40 -40 -40 -40 -40 -40 -40 40 40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 -40 -40 40 40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 40 -40 -40 -40 -40 -40 40 -40 40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 -40 -40 40 40 -40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 -40 -40 40 -40 -40 40 -40 40 -40 -40 -40 12 -12 -40 -40 " and each four number is parted by tab #################################### sub seqprb2std { die("Usage: fq_all2std.pl seqprb2std <in.seq.txt> <in.prb.txt>\n") if (@ARGV != 2); my ($fhs, $fhq); open($fhs, $ARGV[0]) || die; open($fhq, $ARGV[1]) || die; while (<$fhs>) { my @t = split; my $name = join(":", @t[0..3]); $t[4] =~ tr/./N/; print "\@$name\n$t[4]\n+\n"; $_ = <$fhq>; @t = split; my $q = ''; my $max = -100; for (0 .. $#t) { $max = $t[$_] if ($t[$_] > $max); if (($_&0x3) == 3) { $q .= $conv_table[$max+64]; $max = -100; } } print "$q\n"; } close($fhs); close($fhq); } |
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