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Old 02-04-2013, 02:51 AM   #1
Location: Cape Town

Join Date: May 2009
Posts: 19
Default RAD-tag QTL annotation


We are working on a QTL project and we used markers obtained with the RAD method (100 base pair single-end). We built a linkage map and we found some QTLs with both single markers and Interval mapping analysis. We were wondering about the best method to functionally annotate these QTLs. We have a draft genome for the species we are working on, so I would take advantage of this extra info. Two methods I was thinking (and used in other works) are:

1) Blast the RAD-tags on protein databases (but in our case the short length of the markers, 100bp, could be a problem)

2) Blast the RAD-tags against the draft genome and extract the flanking regions of the blast-hit and annotate these long regions (but how many base pairs are reasonable to extract?)

- What do you think about these methods, advantages and drawbacks?

- Can you suggest me a better way to carry on the functional annotation of the QTLs?

Thanks in advance for your help!


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