Visualisation issue with mapped BAM file - how do I find my region of interest...

[TabeaK]

Okay, I am slightly stuck in my illumina analysis, with something that is probably trivial, but I have not figured how out to do it...

Here is what I have done: I have mapped a couple hundred million illumina reads onto my reference genome using BWA and merged all BAM files into one. I have then sorted and indexed the bam file, all using samtools.

My reference genome is from a whole genome shotgun assembly, so it is a whole bunch of contigs/scaffolds lined up in one FASTA file (downloaded from NCBI) including all the gaps (Ns). The scaffolds are unplaced, i.e. I have no idea where the scaffolds are on chromosomes or the like, nor have chromosomal coordinates...

I know, from the reference genome, exactly what scaffold (they are archived separately on NCBI) I am interested in, but not WHERE in the fasta the scaffold is located..

So, in my alignment, how do I find these scaffolds again?

I have been trialling IGV, that works quite well in visualising the data, but it uses the BWA index coordinates from the BAM file, obviously, so I do not know who to "jump" to my region of interest.

Any idea of how to accomplish this? I am willing to trial other tools for visualisation as well.

I hope this makes sense...I am starting to confuse myself.

[TabeaK]

Nevermind! In a typical "duh" moment I have just realised that IGV shows me all the contigs, not the scaffolds. So it should be as easy as piecing together the scaffolds I am interested in...

Anyway, if anyone knows a good tool that allows me to view the whole genome AT A TIME, not click through individual contigs, let me know.