Hi,
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!
Cheers
Paolo
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!
Cheers
Paolo
