Newbler Statistics

Question

[Diogo Santos]

Hello

I've done an assembly with newbler 2.5 under -cdna option. This assembly use reads from 3 diferent sff files. After that I had blasted the results at AllContigs.fasta and I need to know from each sff file come the reads that forma each contig. I've already make this for isotigs+contigs presented in ace file, but is only useful for me if I blast the 454Isotigs file (wich I had already started). But for the sake of comparion to prior experimentes i need to know the results for all contigs, but i can't find a way to know from were each contig came.

Thanks

Answer 1

[lexnederbragt]

The only way you can do this is by using the ace file, and unfortunately, this file does not contain all contigs, only those that didn't make it into isotigs. You could of course write a script that reads in the info on which contigs an isotig is made up of from what to which base (454Isotigs.txt file), and match that with the read info from the ace file etc, but this would be quite some work...

Answer 2

[Fabian Bull]

You should extract the sequences of your sff files using sff_extract.

After this you can use any mapping tool to see which reads map against your assembled reference.