[bioinfosm]

my previous workflow to go from solexa's sequence.txt to maq mapping went like this

maq sol2sanger s_1_sequence.txt w
maq fastq2bfq w reads-1.bfq 2> /dev/null
maq map -u lane1.unmapped reads-1.map maq.bfa reads-1.bfq 2> reads-1.map.log

and i would think that sol2sts2 would run on sequence.txt and the output would directly go to maq map..

[seq_GA]

Can anyone clearly say that with solexa pipeline 1.3.4 output, do we need to convert 'maq sol2sanger s_1_sequence.txt s_1_sequence.fastq' and then proceed to 'maq fastq2bfq' command?

Thanks.

[maising]

The main problem with this new format is that it's now nigh on impossible to tell the difference between phred+64 and logodds+64 formats without resorting to a large amount of statistical analysis on the file contents.

It's easy enough to convert of course, but knowing precisely what format your input data is in is getting trickier by the day. Time for fastq to retire I think!

James

The rationale for moving to phred+64 was that
a) the phred scale is more standard and the logodds don't add much benefit for single quality scores (instead of 4 scores per base)
b) the offset of 64 is what previous versions of the pipeline produced, so the idea was to follow the principle of least surprise.

Also the assumption was that for practical purposes, there is very little difference between logodds and phred when applied to a single quality value, so existing conversion scripts could easily be modified to accommodate qseq files.

Replacing fastq with something better would certainly help.

Cheers
Klaus

Disclaimer: I work at Illumina.

[caddymob]

Thanks for your help on this lparsons and everyone! Kinda sucks I have to go back and rerun some analysis, but thats the beauty of making bash scripts I guess.

EDIT: Just to clarify. Once I do sol2std2 my data is now in standard/Sanger FASTQ format -- I SHOULD NOT do sol2sanger. Right? Think I'm on board...

[Youri]

Ok I'm pretty new to this, and I cant get the code to work (both Iparsons and kmcarr's). I've edited the fq_all2std.pl correctly, but cant get the command right. So what is the exact command that has to be used?

Youri.

[lparsons]

What sort of error are you getting? You should be able to use:

fq_all2std.pl sol2std2 illumina_file.txt > standard_sanger_file.fastq

[maubp]

What sort of error are you getting? You should be able to use:

fq_all2std.pl sol2std2 illumina_file.txt > standard_sanger_file.fastq

Note that alternatively there is Davide Cittaro's patch on the MAQ bug tracker which adds an ill2sanger option to MAQ itself:
http://sourceforge.net/tracker/?func...15&atid=938895

Also the OBF projects (BioPerl, Biopython, BioJava, BioRuby and EMBOSS) already or will support these conversions too.

Peter

[Youri]

Thanks for the replies, apparently there was an mistake in the fastq file, that caused the converter to crash, got it working now.

Again, thanks for the help

Youri