Wednesday

Lab notebook

Note: when linking to a post on another jekyll website, do not include the .html

This does not redirect correctly:

introduction

but this does:

introduction

Go figure.

Aphaenogaster

Still insurance issues with permits for VT, MA and NY. Decided to skip state agencies and contact land trusts (e.g. Trustees of the Reservation in MA) and other privately-owned land with research connections (college field stations).

Contacted Middlebury and immediately received informal permission to sample at their … Forest and Research and Teaching Natural Area.

Sara asked about ordering kits for DGE. Quick calculation:

Contacted NuGENE to ask about updated bulk order pricing.

Computing

set up backup to Amazon S3 using Deja Dup

Bradyrhizobium

Pipeline for bowtie

SAM to BAM using samtools view
use -q to filter reads with MAPQ (mapping quality) > 10, which are probably unique
sort BAM
mpileup to consensus sequence
fastq to fasta using seqtk