SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent



Similar Threads
Thread Thread Starter Forum Replies Last Post
FASTX Toolkit barcode splitter issue jdanderson Bioinformatics 36 01-31-2016 07:09 PM
FastX-toolkit liu_xt005 Bioinformatics 13 10-11-2014 05:52 AM
FASTX-Toolkit: quality score value thinkRNA Bioinformatics 13 09-30-2014 10:25 AM
FastX-Toolkit qual_filter error WaltL Bioinformatics 4 09-10-2012 12:05 PM
Fastx Toolkit for Quality Stats of data from new illumina pipeline software vedbar Bioinformatics 6 09-19-2011 10:50 AM

Reply
 
Thread Tools
Old 10-04-2012, 01:25 PM   #1
gkijak
Junior Member
 
Location: US

Join Date: Oct 2012
Posts: 3
Default Has anyone used FastX Toolkit with IonTorrent data?

Hi y'all,
Has anyone used FastX Toolkit with IonTorrent data? I'm trying to analyze my fastq files and I get errors like:
fastq_to_fasta: Invalid quality score value (char '0' ord 48 quality value -16) on line 4
and something similar with fastx_quality_stats

Am I right at thinking that the problem is that the quality values need to be expressed in the Solexa system and thus FastX won't work with Ion Torrent? That would be a shame...

Thanks,
Gustavo
gkijak is offline   Reply With Quote
Old 10-04-2012, 01:52 PM   #2
mnkyboy
Member
 
Location: Seattle, WA

Join Date: Mar 2009
Posts: 87
Default

I think it is -Q 33 or -Q 64 that specifies which PHRED quality scores it will use. By default it uses the Solexa quals.
mnkyboy is offline   Reply With Quote
Old 10-04-2012, 02:10 PM   #3
gkijak
Junior Member
 
Location: US

Join Date: Oct 2012
Posts: 3
Default

Dear mnkboy,
Thanks for your prompt response.
I do not see the -Q 33 or -Q 64 option either at fastq_to_fasta or at fastx_quality_stats:

usage: fastx_quality_stats [-h] [-N] [-i INFILE] [-o OUTFILE]
Part of FASTX Toolkit 0.0.13 by A. Gordon (gordon@cshl.edu)

[-h] = This helpful help screen.
[-i INFILE] = FASTQ input file. default is STDIN.
[-o OUTFILE] = TEXT output file. default is STDOUT.
[-N] = New output format (with more information per nucleotide/cycle)

usage: fastq_to_fasta [-h] [-r] [-n] [-v] [-z] [-i INFILE] [-o OUTFILE]
Part of FASTX Toolkit 0.0.13 by A. Gordon (gordon@cshl.edu)

[-h] = This helpful help screen.
[-r] = Rename sequence identifiers to numbers.
[-n] = keep sequences with unknown (N) nucleotides.
Default is to discard such sequences.
[-v] = Verbose - report number of sequences.
If [-o] is specified, report will be printed to STDOUT.
If [-o] is not specified (and output goes to STDOUT),
report will be printed to STDERR.
[-z] = Compress output with GZIP.
[-i INFILE] = FASTA/Q input file. default is STDIN.
[-o OUTFILE] = FASTA output file. default is STDOUT.

is there another way to tell the program I'm working on a -Q 64 environment?

Thanks,
Gustavo
gkijak is offline   Reply With Quote
Old 10-04-2012, 02:26 PM   #4
mnkyboy
Member
 
Location: Seattle, WA

Join Date: Mar 2009
Posts: 87
Default

It is not in the documentation, which is why it is confusing. I think the default is -Q 64 and if you use the other you have to do -Q 33. I do not think it supports anything else.
mnkyboy is offline   Reply With Quote
Old 10-05-2012, 07:51 AM   #5
gkijak
Junior Member
 
Location: US

Join Date: Oct 2012
Posts: 3
Default

thanks, mnkyboy! It worked like a charm!
gkijak is offline   Reply With Quote
Old 01-12-2013, 11:45 AM   #6
debasish
Junior Member
 
Location: new delhi,India

Join Date: Sep 2011
Posts: 1
Default

I agree with mnkboy... it is not doccumented ... it even works with recent illumina pipeline...(CASSAVA 1.9 I guess)
debasish is offline   Reply With Quote
Old 05-28-2013, 06:22 AM   #7
vbiaudet
Member
 
Location: Paris

Join Date: Apr 2011
Posts: 13
Default tools for Ion proton quality?

Did you obtain an answer because I have the same problem with Ion Proton reads? or did you use an other tools that fastx?
Thank you vb

Quote:
Originally Posted by gkijak View Post
Hi y'all,
Has anyone used FastX Toolkit with IonTorrent data? I'm trying to analyze my fastq files and I get errors like:
fastq_to_fasta: Invalid quality score value (char '0' ord 48 quality value -16) on line 4
and something similar with fastx_quality_stats

Am I right at thinking that the problem is that the quality values need to be expressed in the Solexa system and thus FastX won't work with Ion Torrent? That would be a shame...

Thanks,
Gustavo
vbiaudet is offline   Reply With Quote
Old 06-05-2013, 06:16 PM   #8
heiya
Member
 
Location: China

Join Date: Nov 2011
Posts: 14
Default

Quote:
Originally Posted by vbiaudet View Post
Did you obtain an answer because I have the same problem with Ion Proton reads? or did you use an other tools that fastx?
Thank you vb
when you use "fastx_quality_stats", you should add "-Q 33", for its default is Illumina's coding format.
heiya is offline   Reply With Quote
Reply

Tags
fastq, fastx toolkit, ion torrent, quality

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 05:49 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO