Redmine

06/07/2018

02:37 PM Setting up a portable 16S rDNA pipeline for CBIO 35.00 hours (Feature #53 (New): Setup a decontamination pipeline for Mark's project)

Samson Kilaza

02:37 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #53: Setup a decontamination pipeline for Mark's project

Hi,
I have prepared scripts for the detection of contaminants [detect.sh] and removal of contaminant [decont.sh] ... Samson Kilaza

11:03 AM Setting up a portable 16S rDNA pipeline for CBIO Feature #54: DADA2 workflow as an additional option for processing 16S data

Good progress Katie, I will make a try at some point.
Samson
Katie Lennard wrote:
> The pipeline is now up a... Samson Kilaza

05/23/2018

01:34 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #53: Setup a decontamination pipeline for Mark's project

Hi,
I have started constructing decontamination module on uct-cbio repository, and have named (uct-cbio/16S-rDNA-... Samson Kilaza

05/18/2018

01:28 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #52: Cleaning up current pipeline outputs for easier management downstream, finalise protocol of metadata sharing between sequencing, pipeline processing and statistical analysis

Hi Gerrit,
I have finished commenting on the google document you have shared.
Samson Samson Kilaza

05/17/2018

03:37 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #54: DADA2 workflow as an additional option for processing 16S data

Yeah, I have tried to run the tutorial dataset online (https://benjjneb.github.io/dada2/tutorial.html) using R on my ... Samson Kilaza

03:21 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #53: Setup a decontamination pipeline for Mark's project

Thanks Samson Kilaza

03:13 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #53: Setup a decontamination pipeline for Mark's project

I have attached some files and steps to be done.
Still, I may clarify if this is not enough
Thanks Samson Kilaza

02:13 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #52: Cleaning up current pipeline outputs for easier management downstream, finalise protocol of metadata sharing between sequencing, pipeline processing and statistical analysis

Hi,
I am working on the shared document.
Samson Samson Kilaza