07 January 2014

blast and RNA extraction

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Tuesday Jan 7


Based on recommendation, used FastAnnotator for annotation - GREAT web resource!

Results for AphVT assembly.

Meeting with Mahesh

Discussed transcriptome assembly and analysis.

Advocates using full (not digitally-normalized) assembly with all reads from both colonies

  1. Using full assembly, identify thermally-responsive genes for both colonies combined
  2. Map reads for each colony individually to subset of thermally-responsive genes
  • prediction: clustering by temperature, not by colony ID


RNA extraction with 3 samples from ApTranscriptome. Trial run and will use these to evaluate DGE against full RNAseq.

Took about 5 hours for complete protocol.

Total yield 140-600 ng per sample. Well above minimum of 10 ng for DGE kit.


Comments to Yun on Medicago GWAS manuscript

Set up blastn job for Chagas on mason cluster

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