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I'm trying to use Maq software but i've face with some problems.
1. Conversion of *qseq.txt files (obtained after demultiplexing) to fastq (illumina) format. For doing this operation i've used this script:
2. Conversion of the "fastq illumina" files just get at point 1 to "fastq sanger format".
For doing this i've tryied to different approaches:
3. After converting reads (fastq sanger) and reference sequence (fasta format) to .bfg and .bfa respectively, i've tried to perform the mapping with the "match command" but i got segmentation fault.
How can solve this problem?
I've tried both 0.7.1 and 0.6.8 version but nothing change.
Which is the faulty step? Where i'm getting wrong?
Thanks in advance!
1. Conversion of *qseq.txt files (obtained after demultiplexing) to fastq (illumina) format. For doing this operation i've used this script:
#!/usr/bin/perl
use warnings;
use strict;
while (<>) {
chomp;
my @parts = split /\t/;
print "@","$parts[0]:$parts[2]:$parts[3]:$parts[4]:$parts[5]#$parts[6]/$parts[7]\n";
print "$parts[8]\n";
print "+","$parts[0]:$parts[2]:$parts[3]:$parts[4]:$parts[5]#$parts[6]/$parts[7]\n";
print "$parts[9]\n";
}
use warnings;
use strict;
while (<>) {
chomp;
my @parts = split /\t/;
print "@","$parts[0]:$parts[2]:$parts[3]:$parts[4]:$parts[5]#$parts[6]/$parts[7]\n";
print "$parts[8]\n";
print "+","$parts[0]:$parts[2]:$parts[3]:$parts[4]:$parts[5]#$parts[6]/$parts[7]\n";
print "$parts[9]\n";
}
For doing this i've tryied to different approaches:
- Patching Maq with maq_ill2sanger.patch
- Using the script called fq_all2std.pl with the command "sol2std"
- Using the script in attachment called qseq2fastqsang.pl
3. After converting reads (fastq sanger) and reference sequence (fasta format) to .bfg and .bfa respectively, i've tried to perform the mapping with the "match command" but i got segmentation fault.
How can solve this problem?
I've tried both 0.7.1 and 0.6.8 version but nothing change.
Which is the faulty step? Where i'm getting wrong?
Thanks in advance!
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