Which format of reads quality is assumed in bfast bwaaln command

[david.tamborero]

Hello,

I am using bfast to align reads (paired-end) from Illumina GAIIx, so the first step is to perform the bfast bwaaln command. I am wondering whether this command assumes that the quality of the reads are Illumina 1.3+ or not, since the -I argument that bwa has to indicate so is not availaible in bfast (or at least, in the bfast+bwa-0.6.4e i am currently using).

By the way, how can I know the version of the BWA used by a certain bfast+bwa release?

Thanks a lot!
David

[nilshomer]

Hello,

I am using bfast to align reads (paired-end) from Illumina GAIIx, so the first step is to perform the bfast bwaaln command. I am wondering whether this command assumes that the quality of the reads are Illumina 1.3+ or not, since the -I argument that bwa has to indicate so is not availaible in bfast (or at least, in the bfast+bwa-0.6.4e i am currently using).

The aim is not to integrate BWA fully into BFAST, but to use BWA (short) to map very short sequences, for example when SOLiD first came out with its paired end kit (50+25), and we wanted to sensitively map the 25bp portion.

Therefore, unless you have short data (less than 35bp), use "bfast match".

By the way, how can I know the version of the BWA used by a certain bfast+bwa release?

Again, no version, as it this functionality is not meant to replicate BWA.

[david.tamborero]

I totally missed that point, sorry for that.

But anyway, regardless of bfast bwaalign or bfast match, the alignement process should take into account the qualities of the reads at some step(s). So still, if they are Illumina (-A 0), how it is known the quality format (for instance, 1.3+ or 1.5+)? It is automatically detected?

Thnks again for your time,

cheers
david