17 April 2014

ddRADseq, null hypothesis, and Bioanalyzer

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Thursday April 17 notes

  • Lucia’s thesis proposal seminar

  • Lab meeting - intro to Mike’s paper


Bioanalyzer results from double digested samples

With Andrew’s help, got the concentration within selected regions (180 - 220 bp, 270 - 330 bp, 360 - 440 bp).

Ln 1, Ap001, is genomic DNA. Note smear above largest marker and no/very little DNA within assay range.

Ln 2 - 6 are double-digested samples. Looks like digest worked well for all samples as concentration in the 180 - 220 bp window ranged from 0.84 - 3.64 ng/ul.


With help from Feder

  1. Install and run deconseq
  • download databases of contaminants
  • open DeconSeqConfig.pm
  • change database directory to where databases are stored
  • couldn’t get script to work if linked from \usr\local\bin\ so just added deconseq to path in .bash_rc
  • run with command

    deconseq.pl -c 50 -i 95 -f Trinity_cap3_uclust.fasta -id Trinity_cap3_uclust -dbs hsref,bast,vir,arch

where -c 50 requires 50% coverage and -i 95 requires 95% similarity to a match in the contaminant database for a read to be considered a contaminant, and -dbs specifies the names (listed in DeconSeqConfig.pm file) of the databases to search as contaminants

  • 5,675 contaminants
  • 99,861 clean

A random 5 contaminants were all BLAST hits to human or bacteria with greater than 95% identity.


Meet with Grace and performed initial analysis of data. Not even no difference, but almost exactly 50:50 foraging among treatments for both experimental colonies! Great demonstration of null result.

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