RNAseq blood profiling of liver fibrosis during schistosomiasis » schistosomiasis metagenomics profiling

# Wiki

# Data location

The data was transferred using Globus connect and Ilifu's Globus endpoint from a PC setup in cbio to Ilifu:

`/cbio/users/katie/Nono/metagenomics
`

The data has already been cleaned and decontaminated (human) by BGI, who have also performed a full analysis on the data (see files section)

The full BGI results can be found together with the cleaned reads on Ilifu.

# YAMP pipeline update
The YAMP pipeline was updated with:
1. with the latest metaphlan DB, downloaded from https://zenodo.org/record/4629921#.Yji3YxNBzOR
2. the latest humann DBs (chocophlan and uniref), as described here https://github.com/alesssia/YAMP/wiki/Getting-started#notes-on-the-metaphlan-databases and first downloading the relevant singularity container with `singularity pull docker://biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7`
The command executed, from within the github directory of the latest YAMP repo was:
`singularity run biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7 humann_databases --download chocophlan full
./assets/data/chocophlan `
AND
`singularity run biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7 humann_databases --download uniref uniref90_diamond
./assets/data/uniref`