[mira_talk] estimation number of genes
- From: Jordi Durban <jordi.durban@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 20 Apr 2012 12:49:11 +0200
Hi all!
I have a question regarding a multistep assembly process:
I had a set of previously annotated contigs from a non-model organism. I
mean contigs, as they resulted from a previous Newbler assembly process.
Those contigs were aligned to a given reference nucleotide sequence in
order to know which of them could be assigned to an open reading frame,
discarding those which fall in UTR regions.
Keeping this in mind, I tried to assembly the contigs with MIRA as an
approach to set a "minimum number of genes" that could be estimated from
these contigs. I mean, those contigs belonging to the same "gene" should
be assembled together, and the debris file should have those "orphan"
contigs, but I don't know if the debris file should be taking into account
as they could be a megahub or repeat masker stuff.
What do you think about such an approach??
What I used in roder to asssembly the contigs was:
mira --project=myproject --fasta --job=denovo,est,454,normal 454_SETTINGS
-LR:mxti=no -LR:wqf=no -CL:qc=yes -AS:epoq=no
Thank you very much.
Jordi
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