Function of defline in fastq format

[maimaiti2008]

Does anyone know what the function of defline starting with '+' in a fastq format file really is except providing some descriptive information? If it does not have any function in downstream analysis, does it mean that we can ignore this line (if we do not care the descriptive information)? I think people can save some space by minimizing the defline.

[dpryan]

It's pretty common to just replace that with a single "+" for the reasons you mentioned.

[Bukowski]

It's a delimiter between the sequence and quality lines. Trust me if you've dealt with enough Fasta like formats over the years that people have mutilated in various text editors (or worse, word processors), you need something more definitive than a linebreak to tell the difference.

There is no requirement for them to match the metadata in the @ line.

[maubp]

There is no requirement for them to match the metadata in the @ line.

That is a minority view. The FASTQ format such as it is requires the '+' line to match the '@' or be left blank. Many parsers will reject it otherwise.

http://en.wikipedia.org/wiki/FASTQ_format

http://dx.doi.org/10.1093/nar/gkp1137

[Bukowski]

That is a minority view. The FASTQ format such as it is requires the '+' line to match the '@' or be left blank. Many parsers will reject it otherwise.

http://en.wikipedia.org/wiki/FASTQ_format

http://dx.doi.org/10.1093/nar/gkp1137

All the HiSeq data I get has no metadata in that line. Is that the default for HiSeqs? In which case it might be a majority view

[dpryan]

All the HiSeq data I get has no metadata in that line. Is that the default for HiSeqs? In which case it might be a majority view

Likewise, at the least it's a very rapidly increasing minority!

[maubp]

Leaving the '+' line blank ought be the norm by now - the disk space saving alone is a compelling argument.

(If my earlier comment was unclear, I'm saying conflicting '@' and '+' lines is non-standard and a bad idea)

[Bukowski]

Leaving the '+' line blank ought be the norm by now - the disk space saving alone is a compelling argument.

(If my earlier comment was unclear, I'm saying conflicting '@' and '+' lines is non-standard and a bad idea)

Ah, that wasn't what I parsed from your comment, thanks for the clarification! And in fact it was my initial comment that was unclear, I should have stated that it could be left blank, not that they shouln' t match. My bad.

[dpryan]

Ah, fair enough!