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Old 03-26-2010, 02:02 AM   #25
Location: Cape Town

Join Date: May 2009
Posts: 19

We did think about reducing genome with some techniques like the one you suggested. We are oriented to transcriptome because we just have some sets Illumina short reads about 40 bp of length and we would like to improve our de novo transcriptome assembly, and with the increased data and depth of coverage obtain a more reliable SNPs detection.

Regarding the suggestions of Iletourn, I tried some preliminary analysis regarding SNPs detection with MAQ and SAMTOOLS and I had some results. The only thing/problem in my sample is the relation between individuals (19 animals but 16 of them are very closely related beeing sibling) and I think it could affect the analyses. What do you think about? As suggested by MattB, 20 animals are sufficient to start,but for genotyping and for linkage map studies the individuals should be not related. Am I correct? What do you think regarding sample composition?
Thanks for all suggestions and comments!
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