Redmine

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

05/22/2018

05:13 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

Ok Samson I've asked Shantelle also to give some input in the document. Once she has done all of us can maybe meet an... Gerrit Botha

02:12 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #54: DADA2 workflow as an additional option for processing 16S data

Hi Katie,
I think it is definitely better to keep the config and code separate as the RNASeq Nextflow pipeline. Fo... Gerrit Botha

01:54 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #54: DADA2 workflow as an additional option for processing 16S data

Gerrit I see the Nextflow implementation of DADA2 currently only consists of one .nf file, no configs etc. Shall I tr... Katie Lennard

05/21/2018

04:47 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 Samson,
I started looking at the document and added some comments on request. Can you please have a look.
Ge... Gerrit Botha

05/18/2018

01:41 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

Thank you Samson, I will have a look and get back to you.
Gerrit Gerrit Botha

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

02:52 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #54: DADA2 workflow as an additional option for processing 16S data

Hi Katie,
I've forked the HPCBIo repos to here: https://github.com/uct-cbio/16S-rDNA-dada2-pipeline . I've given y... Gerrit Botha

02:20 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #54: DADA2 workflow as an additional option for processing 16S data

Hi Gerrit,
Yes I'm keen to help with this and test on the WISH dataset.
Katie Lennard

02:09 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #54: DADA2 workflow as an additional option for processing 16S data

Katie and Samson,
Chris has made their DADA2 Nextflow pipeline available here: https://github.com/HPCBio/dada2-Nex... Gerrit Botha

02:05 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #54 (New): DADA2 workflow as an additional option for processing 16S data

As mentioned in the description of this project non OTU picking methods such as DADA2 seems to be the choice of many ... Gerrit Botha

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

03:14 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #53: Setup a decontamination pipeline for Mark's project

Thank you Samson, I will have a look and get back to you. Gerrit Botha

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

02:12 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #53: Setup a decontamination pipeline for Mark's project

Reply from Samson on email
-----
*I am finalizing a README file, giving details of steps done for everyone to ... Gerrit Botha

01:59 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #53: Setup a decontamination pipeline for Mark's project

Hi Samson,
Please send me an example of the files you currently use to manually calculate the OTU adjustments and ... Gerrit Botha

01:56 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #53 (New): Setup a decontamination pipeline for Mark's project

All 16S analysis from Mark's project follows an additional QC protocol that was originally suggested by guys from JCV... Gerrit Botha

02:54 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex

Katie I've renamed the repos to https://github.com/uct-cbio/RNAseq-pipeline . In your Git config you just need to mod... Gerrit Botha

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

01:43 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 Samson,
I've uploaded the document Sugnet has shared with me regarding the issues that she is currently experie... Gerrit Botha

01:37 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #52 (New): Cleaning up current pipeline outputs for easier management downstream, finalise protocol of metadata sharing between sequencing, pipeline processing and statistical analysis

Gerrit Botha, Nicki Tiffin and Ray Moholisa had a discussion with Mark Nicol and Sugnet Lubbe regarding their needs i... Gerrit Botha

05/16/2018

02:41 PM Setting up a portable metagenome assembly pipeline for CBIO Support #50: Validate binning using single copy core genes

checkM successfully run on hex. Example outputs listed under the 'Files' tab (checkm.e1851691.txt and checkm.o1851691... Katie Lennard

05/11/2018

11:37 AM Setting up a portable metagenome assembly pipeline for CBIO Support #50 (New): Validate binning using single copy core genes

The quality of the binning results from CONCOCT can be examined by looking at single copy core genes (i.e. genes that... Katie Lennard

05/08/2018

04:03 PM Testing Redmine project features Support #7: Support ticket 1

Just testing adding update as another user (non admin privileges). Want to see if I can edit afterwords.
Ok enable... Gerrit Botha2