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. 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

``` c `singularity pull docker://biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7`
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:

``` c
(base) katiel@compute-004:/cbio/users/katie/Nono/YAMP$ singularity `singularity run workflows_3.0.0.a.6.metaphlanv3.0.7.sif biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7 humann_databases --download chocophlan full
./assets/data/chocophlan `
Creating directory to install database: /cbio/users/katie/Nono/YAMP/assets/data/chocophlan
Creating subdirectory to install database: /cbio/users/katie/Nono/YAMP/assets/data/chocophlan/chocophlan
Download URL: http://huttenhower.sph.harvard.edu/humann2_data/chocophlan/full_chocophlan.v296_201901.tar.gz
Downloading file of size: 15.30 GB

8.37 GB 54.74 % 8.16 MB/sec 14 min 28 sec
15.30 GB 100.00 % 8.30 MB/sec 0 min -0 sec
Extracting: /cbio/users/katie/Nono/YAMP/assets/data/chocophlan/full_chocophlan.v296_201901.tar.gz

Database installed: /cbio/users/katie/Nono/YAMP/assets/data/chocophlan/chocophlan

Unable to write to the HUMAnN config file.
```

AND
`singularity run biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7 humann_databases --download uniref uniref90_diamond
./assets/data/uniref`