Hello everyone,
I'm fairly new to bioinformatics and I am a little stuck. Essentially, I am trying to visualize really large deletions in mutant bacterial genomes (~300,000 base pairs) compared to a reference. I have confirmed the presence of these deletions using the program breseq. After doing so, I have used SPAdes to assemble contigs for each of my mutants, and then uploaded this data to RAST. I then attempted to use the BRIG software, which should align the mutants to the reference genome and show a large blank gap of 300,000 base pairs where the deletion occurred. However, I am getting regions of similarity within the section that should be blank. I was wondering if something sounds wrong with my process, or if anyone has any recommendations for software that could be used to create figures illustrating large genomic deletions instead of BRIG? Thank you in advance for the help.
BRIG doesnt do what you think it does.
BRIG just uses BLAST to generate a list of matching subsequences, and then renders these matches by coordinate relative to the reference sequence at the centre of the circle. If you’re seeing regions of match inside your large deletion, that will most likely be because there is another similar stretch of sequence else where in the mutant genome, that matches against the undeleted span in the reference genome.
You can likely get around this to some degree by increasing the BLAST identity threshold.
This makes a lot more sense now. Thank you for the reply!
http://genomeribbon.com/
This looks like it could be extremely useful. Thank you for the recommendation!
Filter the assembly to remove contigs with very low or very high coverage. What happens if you blast the 300kbp deleted region against the remaining genome? Do you get some hits?