Question: illumina reads - dots vs. 'N's
0
gravatar for Richard
4.7 years ago by
Richard550
Canada
Richard550 wrote:

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!

fastq illumina • 964 views
ADD COMMENTlink written 4.7 years ago by Richard550

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

ADD REPLYlink written 4.7 years ago by Devon Ryan90k
0
gravatar for Istvan Albert
4.7 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

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

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by Istvan Albert ♦♦ 80k
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