Redmine

05/22/2018

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

05/17/2018

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

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

04/30/2018

11:42 AM Setting up a portable metagenome assembly pipeline for CBIO Bug #46 (New): Read binning with CONCOCT

CONCOCT “bins” metagenomic contigs. Metagenomic binning is the process of clustering sequences into clusters correspo... Katie Lennard

04/26/2018

04:39 PM Setting up a portable metagenome assembly pipeline for CBIO Support #45 (New): Quality trimming with Trimmomatic

In short after a bit of a struggle to optimize parameters for quality trimming with Trimmomatic I recommend rather us... Katie Lennard

09:51 AM Setting up a portable metagenome assembly pipeline for CBIO Support #27: What we already know and have setup

Thanks Gerrit,
This workflow https://bitbucket.org/berkeleylab/metabat is also an option - it is dockerised, uses ... Katie Lennard

04/25/2018

12:57 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex

Thanks Gerrit,
Will go through the results and see at which steps we might want to adjust parameters. Yes it's fin... Katie Lennard

10:51 AM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex

Test run completed successfully! Input and output at /researchdata/fhgfs/katie/NGI-RNAseq-test/ (permissions open to ... Katie Lennard