illumina reads - dots vs. 'N's

Question

[Richard]

Hi all,

I'm looking for a bit of a history lesson. Its been a while since I've seen this, but I recall that there was a time when fastq files (or qseqs) contained dots in place of uncalled bases where now there will be an 'N'.

Does anyone know when the transition was made?

Also, can most major aligners handle both '.' and 'N' in place of an uncallable base?

Some aligners I'm interested in:

• BWA
• Bowtie
• Novoalign
• Star
• SNAP

Any information on the topic would be helpful.

Thanks!

[Devon Ryan]

Aren't the dots a color-space thing? At least that's the only place I remember seeing them.

Answer 1

[Istvan Albert]

I don't know about dots but many aligners will insert a random base for the N. Whether that counts as "handling it" depends on the needs of the user.

Come to think of it the one aligner that I know to handle N and other ambiguous bases is lastz

Kind of dovetails nicely into today's topic of: Bob Harris of the LASTZ aligner uses this