Lucia’s thesis proposal seminar
Lab meeting - intro to Mike’s paper
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
\usr\local\bin\so just added deconseq to path in
run with command
deconseq.pl -c 50 -i 95 -f Trinity_cap3_uclust.fasta -id Trinity_cap3_uclust -dbs hsref,bast,vir,arch
-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
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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