Nice github guide
Finished fourth extraction and pooled all together.
Sent Ap001 DNA sample to Delaware Biotechnology Institute for PacBio and Illumina sequencing.
Sample: Aphaenogaster picea ant collected from Molly Bog, VT
DNA was extracted from 4 sets of 20-40 ants using Qiagen DNeasy kit. Elutions of 300-400 ul per exctraction were pooled for a total volume of about 1300 ul.
Nanodrop quantification showed 15.5 ng/ul with a 260/280 ratio of 1.8. Approximate total of 18 ug DNA.
Took required ethics training course for NSF grant at [https://www.citiprogram.org/]
Writing group from 9-10. Added about 700 word to Methods sections of Aphaenogaster transcriptome paper!
Results of BLASTING known spike-in transcripts to A22 assembly:
Metric | Result |
---|---|
Number spike-in | 100 |
Mean length spike-in (bp) | 865.28 |
Number assembled | 99 |
Mean length assembled (bp) | 872.26 |
Mean length missing (bp) | 174 |
Mean proportion of original transcript mapped | 0.97 |
Mean number assembled transcripts per starting | 1.2 |
Proportion bp assembled to starting bp | 1.06 |
Very nice results!
Set up shell script knit on home/scripts
on workstation, symbolic linked in usr/local/bin
such that globally accessible. Problem that R libraries not installed globally…copied my libraries to /usr/local/lib/R/site-library/
following Administration and Maintenance of R packages. To globally install package, start R as super-user
sudo R
and install packages to global library
install.packages("aster2", lib="/usr/local/lib/R/site-library")
Confirmed that the sim.assembly.eval
function fails to find any siginificant matches to the VGN Trinity full data assembly that did not include simulated reads!
Using CAP3 or CD-HIT gives similar results (Yang and Smith 2013) so use only CAP3. As I’m now merging contigs within a species, increase similarity threshold to 98%. Previously used 90% when trying to merge orthologs among species.
Found error - removed trimclip
directory with filtered reads, but need these reads for gene expression quantification!
To check reproducibility of script and get these reads, cloned repo into /home/projects/climate-cascade/projects/ApTranscriptome
and ran
knit ApTran_assemble.R
to start assembly…
2013-12-12 9:26
/scripts (master *)$ nohup nice -n 19 knit ApTran_assemble.R & [1] 12512 nohup: ignoring input and appending output to `nohup.out’
Updates to script
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