454 reads mapping to more than one scaffold?

[Marcela Uliano]

Hey guys, I've been struggling with this question for a while, since I don't program very well.

So, I've mapped some 454 contigs to a very fragmented draft genome (a lot of scaffolds), and I would like to access the quality of this draft by:

1-) Computing how many 454 contigs have mapped to different scaffolds (to investigate how fragmented the draft is)
2-) Computing the alignment length and identity of each aligned 454 contig..

I've mapped with BWA and I have sam, bam and index files.

Can I find these infos with samtools? Or should I use something else?
Thank you so much!

[Brian Bushnell]

I don't see how mapping would be particularly illuminating in this situation. You can generate information on both contig and scaffold continuity with the BBMap suite:

stats.sh in=genome.fa

Alternatively, Quast will generate some nice graphical plots genome size versus number of contigs, but I can't remember if it breaks it down by both contigs and scaffolds.

[Marcela Uliano]

Thank you Brian!

Well, I know that the genome I'm assembling has a high amount of repetitive regions and I have the stats for this first draft, its still pretty bad.

The thing is I have some complete (and some long genes) for such genome generated with 454 technology a couple of years ago. So, by having a look if such sequences would map perfectly inside big scaffolds, or the mapping would be fragmented and to multiple scaffolds, could help to give me an idea of the challenge I'm facing (mostly in terms of the location of the repetitive sequences)!

[Brian Bushnell]

To clarify -

What clade are you working on?

And do you have 454 RNA-seq genes, or genes predicted from assembly of 454 DNA reads?

[Marcela Uliano]

Hi Brian, its a Mollusk!

And I have RNA (cDNA) sequenced with 454 and assembled!