finding overlaps of two transcriptomes/genomes
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What do you mean by overlaps? What are you actually looking for biologically and what did you try out?
Could you please phrase your question better?
I mean overlapping sequences in two transcriptomes. I did transcriptome assembly of two species separately, and I want to find overlaps (sequences) in the two transcriptome. I have not tried any thing yet, just I want to know which approach/method/tool will be better or efficient. Then, I will use only one transcriptome for further analyses.
what do you mean with overlapping? You mean find transcripts of homologous genes?
I mean overlapping sequences in two transcriptomes.
Well, this is what you already wrote in the post, and it is actually not really clear.
Overlap can be total/partial/with errors and gaps. You need to specific about what you are willing to tolerate.
Take a look at dedupe.sh from BBMap to see if that would help.
Dear Mehmet, Hi
Are you trying to find out that which transcriptomes are present exactly in both assemblies ? (and what next ?)
Or you want to compare the overlap between the mRNA of a selected gene in one transcriptome with the other one ?
~ Best
Hi Farbod:
My point is to find how similar two assemblies in terms of sequences. if two assemblies are quite similar (similarly is high), I will use one of them for next (annotations, pathways etc).
thanks.
Dear Mehmet, Hi.
If I get the point correctly, you have two transcriptome assemblies with the same design (# of replication, same species, same instrument and . . . ) and you do not know which one to use.
May be you should use DETONATE, BUSCO, or check if you have "sequenced deeply enough to generate a high quality assembly", to select the "better" assembly.
The blasting approach that Tereza has used for comparing assemblies is an acceptable one, in my opinion.
Search for "The three candidate assemblies were evaluated by BLASTn" in her paper, please.
~ Take care
Thank you. Yes, you did understand correctly. Is it possible to find overlapping using blast ?
I guess what you mean is to look for orthologs between your two transcript assemblies. This might help, also Proteinortho is easy to run on your data.
No, I mean I have two transcriptome assemblies. I want to compare the two assembly and to find overlapping sequences.
So if I get it right, you are comparing two assemblies from the same source, and need the most conserved ones. I wouldn't see it much different from an ortholog search with high identity and coverage filtering.