23 December 2013

transcriptome, Trinity, knitr, and pandoc

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Monday notes

Holiday week! Feeding ants today and Friday.


Wrote function rename.trinity.transcripts to rename transcripts generated from Trinity after assembling with CAP3. More complicated than I orginally though as I had to

  • rename both
  • CAP3 assembled contigs with header Contig1
  • CAP3 singlets with format >comp77763_c0_seq1 len=213 path=[102682384:0-212]
  • maintain alternative transcript (seq) information from trinity
  • comp118_c0_seq1 len=230 path=[42071:0-80 42152:81-229]

  • comp118_c0_seq2 len=207 path=[42600:0-57 42152:58-206]

  • while allowing for over 100 (wtf???) alternative transcripts in some cases


While pandoc is great, the default options to generate a pdf from markdown are terrible. Wrote a script md2pdf that provides some useful options to pandoc to improve pdf output. For this and other useful scripts, created a “toolbox” directory and repository on github.

Added a number of R script and latex templates to this repository.

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