Feature #53
Setup a decontamination pipeline for Mark's project
Description
All 16S analysis from Mark's project follows an additional QC protocol that was originally suggested by guys from JCVI. During sequencing they also add controls (OTUs) which needs to be subtracted from environment microbial OTU's before statistical analysis can continue on the BIOM file.
Samson has been looking into this. Currently some steps are scripted but other steps currently require's some manual labour.
The plan is now to fully automate this process and make the pipeline available on the uct-cbio GitHub space.
Files
History
Updated by Gerrit Botha almost 7 years ago
Hi Samson,
Please send me an example of the files you currently use to manually calculate the OTU adjustments and also a brief summary of your process. I will see if we can script that.
Gerrit
Updated by Gerrit Botha almost 7 years ago
Reply from Samson on email
I am finalizing a README file, giving details of steps done for everyone to easily understand
Samson
Thank you Samson. At the moment replying on emails do not automatically update tickets. Best to rely directly from the Redmine interface.
Gerrit
Updated by Samson Kilaza almost 7 years ago
- File mapped_contaminant.txt mapped_contaminant.txt added
- File otu-table.txt otu-table.txt added
- File Spiked_control.txt Spiked_control.txt added
- File steps.docx steps.docx added
- File steps.pdf steps.pdf added
I have attached some files and steps to be done.
Still, I may clarify if this is not enough
Thanks
Updated by Gerrit Botha almost 7 years ago
Thank you Samson, I will have a look and get back to you.
Updated by Samson Kilaza almost 7 years ago
Hi,
I have started constructing decontamination module on uct-cbio repository, and have named (uct-cbio/16S-rDNA-decon-pipeline) as per the previous meeting. I have as well alerted as being under construction till everything is tested to be fine.
Samson
Updated by Samson Kilaza almost 7 years ago
- % Done changed from 0 to 90
Hi,
I have prepared scripts for the detection of contaminants [detect.sh] and removal of contaminant [decont.sh] from the target biological samples, and updated in uct-cbio/16S-rDNA-decon-pipeline. The remaining part is a script for finding the average and profile comparison of reads in spiked controls.