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Old 08-10-2009, 08:28 AM   #1
Tombre
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Location: Durham, UK

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Default 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
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Old 08-20-2009, 10:13 AM   #2
jwhittall
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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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