ASV Tables Created in R
ASV tables created using the Bioconductor/R version of DADA2 are matrix files with samples as rows and taxa as columns. The taxa names are the sequences themselves. Because these matrices can be quite large they are most conveniently saved as compressed rds files. Read these files into R and create an experiment level phyloseq object containing an OTU or ASV table and representative sequences with the following R script: Continue reading “Import DADA2 ASV Tables into phyloseq”
If you need to know the execution time for a bash script, you can place it inside the script below. The the total run time will be printed to the screen after the script finishes. Continue reading “Get Execution Time for a Shell Script”
Gedit is the basic editor that is included in Ubuntu and other Linux distributions. Its functionality can be extended with plugins as explained in the post below. I installed the plugin initially because it allows one to comment or un-comment selected lines of text. I find this useful when I want to include two configuration blocks in a script, say one for a local installation of a program and another for a remote installation on a cluster. If you do this, just make sure the appropriate blocks are commented and un-commented when you run the script.
Source: Code Comment – gedit Plugin | Delightly Linux