Number of runs required SNP detection transcriptome

Tombre · 08-10-2009, 09:28 AM

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, 11:13 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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08-10-2009, 09:28 AM	#1
Tombre Junior Member Location: Durham, UK Join Date: Aug 2009 Posts: 1	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

08-20-2009, 11:13 AM	#2
jwhittall Junior Member Location: Santa Clara, CA Join Date: Aug 2009 Posts: 2	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