Re-working the analysis

I have been going back into my transcriptomes for each plant and pulling out ‘genes’ that fit with Hidden Markov Models I made using HMMER ( I used the specific domains from resistance gene models, previously identified in Eucalyptus grandis ( and chitinases ( to initially find putative genes in my clustered Syzygium. Then I used the aligned genes to build species specific nucleotide HMM for several defence-related genes.

Armed with lists of potential genes in each transcriptome I now want to find out if there are actually transcript variations between my resistant and susceptible plants.

This has meant aligning my raw reads for each plant/at each time against its own transcriptome. A big job again – hope it is worth it.

Another thing that has been useful recently is the regular expressions for sorting etc in Notepad +++ ( With large datasets it seems there is always something needing extracting or amending.

Have a bunch of primers ready as well to check against all samples. Back to the lab soon for much qRTPCR.


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