Grace’s Notebook: Reading up on Trinity and Interviewed Genevieve Johnson for DecaPod

Today I did more reading on how to start assembling a transcriptome using Trinity with plans to formulate the beginning steps tomorrow and I interviewed Genevieve Johnson (University of Alaska, Fairbanks) on her thesis project doing Tanner Crab population genetics for a new soon-to-be published episode of DecaPod.


I read a lot of cool things about Trinity and here are some links to useful information:
Main Trinity wiki:
RNAseq Workshop slides:
Trinity de novo Transcriptome assembly workshop:

DecaPod S1E9

Genevieve Johnson stopped by today (she’s in Seattle for a conference) and I recorded her sharing her experience performing her thesis work on population genetics of Tanner Crabs of Alaska. It was a really good interview and she is very good at communicating, so I won’t have to spend too much time editing and publishing! Will be published either tonight or tomorrow! Woo!

from Grace’s Lab Notebook

bismark ran on mox -…

bismark ran on mox – default – 6 hours
might play with multicore option

[sr320@mox2 0620]$ cat *report.txt | grep "Mapping"
Mapping efficiency:	35.8%
Mapping efficiency:	34.8%
Mapping efficiency:	35.0%
Mapping efficiency:	35.9%
Mapping efficiency:	34.3%
Mapping efficiency:	34.0%
Mapping efficiency:	35.4%
Mapping efficiency:	33.6%
[sr320@mox2 0620]$ head slurm-194366.out 
Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/bowtie2 --version' [2.1.0])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools'
Reference genome folder provided is /gscratch/srlab/sr320/data/olurida-genomes/v081/	(absolute path is '/gscratch/srlab/sr320/data/olurida-genomes/v081/)'
FastQ format assumed (by default)
Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4
Each Bowtie 2 instance is going to be run with 28 threads. Please monitor performance closely and tune down if needed!

Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/0620'):