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Old 03-25-2010, 06:10 AM   #22
pfranchini
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Location: Cape Town

Join Date: May 2009
Posts: 19
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Thanks for the info.

Actually, we were wondering to sequence the transcriptome to obtain a higher coverage and find more SNPs as possible to use them in genotyping and for linkage map studies.
We are more interested in most common SNPs and no in rare ones, for this reason we thought to use many animals and optimizing costs using less lanes as possible of a single Illumina run.
We just have a preliminary transcriptome obtained by three Illumina lanes (short reads single and paired of about 40-45 bp) for a total of 18 different animals but closely related. The coverage of the contigs file we built with Velvet is around 30X. Theoretically, should be these data a good starting point to detect SNPs?
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