SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
soap segmentation fault scami Bioinformatics 6 04-17-2012 06:08 AM
cufflinks segmentation fault help please seq_newbie Bioinformatics 1 06-29-2011 11:52 AM
Maq: Segmentation Fault mrxcm3 Bioinformatics 2 03-21-2011 02:43 PM
SOAP:segmentation fault Mansequencer Bioinformatics 1 11-19-2010 10:47 AM
MAQ - Segmentation fault dukevn Bioinformatics 1 04-30-2009 12:07 PM

Reply
 
Thread Tools
Old 02-14-2011, 11:56 PM   #1
Seq84
Member
 
Location: Italy

Join Date: Feb 2011
Posts: 19
Default Maq Segmentation fault

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:

Quote:
#!/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";
}
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:
  • 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!
Attached Files
File Type: txt Line formats (qseq,fastq(ill, sanger).txt (701 Bytes, 4 views)
File Type: pl script_qseq2fastqsang.pl (547 Bytes, 3 views)
Seq84 is offline   Reply With Quote
Old 02-15-2011, 03:09 AM   #2
Seq84
Member
 
Location: Italy

Join Date: Feb 2011
Posts: 19
Default

I've solved the problem

Greetz
Seq84 is offline   Reply With Quote
Old 03-23-2012, 10:17 AM   #3
Fedster
Junior Member
 
Location: London

Join Date: Mar 2012
Posts: 5
Default

Quote:
Originally Posted by Seq84 View Post
I've solved the problem

Greetz
How? I'm having the same issue
Fedster is offline   Reply With Quote
Old 07-13-2012, 04:05 AM   #4
swjh
Junior Member
 
Location: Guangzhou

Join Date: Dec 2010
Posts: 1
Smile solve method

Quote:
Originally Posted by Seq84 View Post
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:
  • 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!
you can split the raw reads to two or three parts and then convert the format to bfq,following,do mapping.After finishing these work,you can merge the mapping result to one file.Hope you to solve the problem soon .
swjh is offline   Reply With Quote
Reply

Tags
maq, maq problem, qseq, segmentation, segmentation fault

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:30 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO