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-   -   Number of runs required SNP detection transcriptome (http://seqanswers.com/forums/showthread.php?t=2290)

Tombre 08-10-2009 08:28 AM

Number of runs required SNP detection transcriptome
 
Hello,
I am just planning my first use of Solexa/Illumina sequencing.
I'm hoping to use this to sequence the transcriptome of a non-model small mammal in order to identify SNPs. RNA from several different individuals and tissues would be pooled for sequencing.
Can anyone tell me, approximately how many sequencing runs I would need to obtain adequate coverage in order to do this?
Thanks very much,
Tom

jwhittall 08-20-2009 10:13 AM

Tom,

No answer here, but I'm in a similar boat and was waiting to see if anyone had an answer to your question. I've got a mustard that is 85-90% similar in nucleotide sequences of coding regions to Arabidopsis thaliana. I think I'll need to assemble de novo, then tBlastx my contigs to the Arabidopsis unigenes. Has anyone tried this for transcriptomes of non-model (but close to model) systems?

Justen


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