Monday notes

Holiday week! Feeding ants today and Friday.

ApTranscriptome

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

Computing

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.