Ran dipSpades for a diploid fungus genome -- now what?

Question

[Lina F]

Hi all,

I successfully ran dipSpades for a diploid fungus genome but now I am feeling stuck on how to analyze the resulting output.

I got the following results:

consensus_contigs.fasta -> 300 contigs
paired_consensus_contigs.fasta -> 216 contigs
unpaired_consensus_contigs.fasta -> 84 contigs

Do you have any advice for how to continue with the analysis beyond running dipspades?

Specifically, I am wondering where or the how the phasing information is stored.

For example, on the manual's website, it states "paired_consensus_contigs.fasta - file in FASTA format with a subset of consensus contigs that have a polymorphism detected on them".

So if I compare the contigs from consensus_contigs.fasta and paired_consensus_contigs.fasta that have the name, does that provide me with SNP information?

Thanks for any suggestions!

[GenoMax]

Is the genome diploid highly polymorphic which is what dipSpades is specifically designed for? What are you exactly hoping to get from this genome?

[Lina F]

Yes, my lab folks tell me it is considered to be a highly polymorphic diploid given dipSpades's definition ("haplomes that differ from each other by 0.4–10%".).

Ultimately, I'm trying to get a somewhat reliable reference with phasing information. The final assembly should be about 16 megabases. I currently have the following number of bases:

consensus_contigs.fasta -> 8,917,627 bases
paired_consensus_contigs.fasta -> 8,389,861 bases
unpaired_consensus_contigs.fasta -> 527,766 bases

[Morgan S.]

Hi OP,

Did you ever figure out what was best to do? I feel stuck after doing genome annotation with MAKER. I used the consensus_contigs.fasta file for downstream analysis, but I am not sure if this is the right file to have proceeded with. I feel like there are a lot of duplicated genes reported from MAKER, which I don't want to skew my results.

Thanks, Morgan

[Lina F]

Unfortunately, I couldn't figure out what the best thing to do was. None of the advice I found on the internet made me feel confident in dipSpades :-(