Has anyone used FastX Toolkit with IonTorrent data?

[gkijak]

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

[mnkyboy]

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.

[gkijak]

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 ([email protected])

[-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 ([email protected])

[-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

[mnkyboy]

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.

[gkijak]

thanks, mnkyboy! It worked like a charm!

[debasish]

I agree with mnkboy... it is not doccumented ... it even works with recent illumina pipeline...(CASSAVA 1.9 I guess)

[vbiaudet]

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

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

[heiya]

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.