30 May 2013
field work, seqtk, Aphaenogaster, Pogonomyrmex, and transcriptomicsNext post Previous post
Seems that the world of (open-source) webapps is never-ending. Just discovered dillinger. Browser-based app that allows side-by-side editing of markdown file and rendered output. While using it now, don’t see it as a long-term solution because CONSIDERABLY slows typing (what’s the point of a flat text file if not fast?) and once you’ve learned the basic markdown syntax, you don’t need to see the output simulatenously.
Also found some information on slidify which may be even better than slides (for me) because it’s based on R code. Though…I’m not sure I want to be creating plots while making a presentation. Seems better to have an .Rmd tech report, then load the images into presentation using slide, slideous, etc.
Comments from NG on P-value commentary.
Finished Functional Ecology review.
Phone call with PT to discuss ‘Estimating heritability using genomic data’ manuscript
Working on transcriptome pipeline with Pogo data
based on fastq files, single reads in Illumina 1.3 format so need to convert
install biopython on antlab
first had to install numpy and scipy using pip
back to some basics for running a job on a server
nohup to run job without hangups, end line with
& to run in background
nohup nice -n 19 bash 01-fastq-sanger.sh
shell script that drives python script
Installed seqtk on antlab as on 2013-05-14.
Damn file format issues.fastx-toolkit assumes Illumina 1.3+ FASTQ (ASCI offset of 64) but thankfully on seqanswers it is explained that there is an undocumented argument -Q that determines the input quality ASCII. This can be changed to
-Q 33 to get standard sanger FASTQ.
Some information about trimming Illumina adaptor sequences
Overwhelming list of bioinformatics papers to read on same website
Wow - email blowing up with responses from ecolog to participate in stats survey, and re-post of Early Career Ecologists blog post by Jeremy Fox at Dynamic Ecology!
Ant collecting at Molly Bog with AN, MH, Keri Pinder
Found 12 colonies in about 4 hours of searching (including bush-whacking through ticket). Only 3 with queens. Easier to find queens from colonies in logs than in leaf debris so target these.
Meeting with Josh Brown
Meeting with VGN: Jim Vincent, Heather Driscoll, Mahesh
choice of de novo assembler
pool all files to generate transcriptomes
population genetic analyses
Jiang, L., F. Schlesinger, C. A. Davis, Y. Zhang, R. Li, M. Salit, T. R. Gingeras, and B. Oliver. 2011. Synthetic spike-in standards for RNA-seq experiments. Genome Research 21:1543–1551.
Redmine for project management. Possible to integrate with github
NuGEN Encore Rapid Kits arrived.
Transferring transcriptome data to VGN.
While disappointed not to find complete data for a recent paper published in Nature (actually not required for field data), I was excited to see their new reporting requirements which state that ‘Sample size’, ‘Randomizaton’ and ‘Replication’ need to be explicitly reported, as well as clear guidelines for statistics!
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