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Old 03-09-2018, 09:13 AM   #291
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Join Date: Feb 2008
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@cb841011: Since this was also cross-posted and discussed on Biostars I will add a reference to the thread here:

You could always use a closely related grass genome (if one is available). There would be some loss of real data (or gain of false positives) but since you don't have the genome of your grass it is about the best you can do.

Since you have
Draft genome of the fungus
RNA-seq reads from non-infected grass
RNA-seq reads from infected grass (contains grass and fungal transcripts)
RNA-seq reads from the fungus growing in culture
You could assemble transcriptomes (using Trinity) from non-infected grass and then fungus. Use those to see if you are able to find any new transcripts showing up in the infected grass.
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