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[Arthropod] EST assembly from Illumina

Don Gilbert via arthropod%40net.bio.net (by gilbertd from cricket.bio.indiana.edu)
Wed Dec 9 13:58:17 EST 2009


Assembling short read RNA-Seq to full mRNA without a reference
genome is harder. If you have longer (72+ bp) mate-paired reads
it become easier than with shorter, single reads.  Here is some
discussion of this

> We're thinking of doing some gene expression analyses for a species on which we have no sequence data and the
>  closest sequenced relative is 100+ million years away.
> I'm thinking it may be possible to do everything in one shot:
>         1. RNAseq (using Illumina)  on our 2 conditions of interest
>         2. Assembly of the RNAseq data to get good gene models -> annotate
>         3. "classic" RNAseq analysis where to identify differential expression 
> The alternative would be to first perform some 454 of a normalized library to get a good overview of the tran
> scriptome.

Software assemblers for this (which I've not used)
include Velvet, newbler, SOAP, probably others.  

Your expression analysis  will depend on having large enough
transcript assemblies to distinguish genes.  And you can expect
a large fraction of differential expression to be in species/clade-specific 

Another approach, you might ask folks on this list if anyone
is sequencing your ant genome, and would like to
collaborate w/ your EST/RNA-seq data.

- Don Gilbert
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd from indiana.edu--http://marmot.bio.indiana.edu/

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