Hello all,
My supervisor and I recently jumped on the next gen bandwagon. Another professor in our department purchased lanes on an RNAseq plate and couldn't fill the entire thing so we took 4 spots. We are working on glyphosate resistant giant ragweed; for which there is no reference genome and little to no genetic data available.
We have a few questions:
1) What do you recommend we do now?
2) In addition to the whole transcriptome date we are also interested specifically in looking at the expression of two or three genes (Catalase, SOD1 Cu/Zn, and EPSPS) however we don't have giant ragweed sequences for those genes. Can we search our data for those genes and their expression levels or is that just out of the question?
3) This data will not be in my MSc and I won't be doing much work with it beyond posting here; but I would like to include a short section in my thesis on the data we collect here. Is it possible to get average read lengths, fold number and other quality statistics about the data to include in my thesis, or does that not make any sense?
Thanks everyone,
Taylor
My supervisor and I recently jumped on the next gen bandwagon. Another professor in our department purchased lanes on an RNAseq plate and couldn't fill the entire thing so we took 4 spots. We are working on glyphosate resistant giant ragweed; for which there is no reference genome and little to no genetic data available.
We have a few questions:
1) What do you recommend we do now?
2) In addition to the whole transcriptome date we are also interested specifically in looking at the expression of two or three genes (Catalase, SOD1 Cu/Zn, and EPSPS) however we don't have giant ragweed sequences for those genes. Can we search our data for those genes and their expression levels or is that just out of the question?
3) This data will not be in my MSc and I won't be doing much work with it beyond posting here; but I would like to include a short section in my thesis on the data we collect here. Is it possible to get average read lengths, fold number and other quality statistics about the data to include in my thesis, or does that not make any sense?
Thanks everyone,
Taylor
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