Commit 64ffc22d authored by Valentina Galata's avatar Valentina Galata
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notes: metap: added credentials for (raw) data access; updated readme for reprod. (issue #127)

parent 9c650220
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# Setup
## Data
Processed sequencing data of the GDB sample is available under BioProject accession PRJNA723028 (Biosamples: metag_sr: SAMN18797629, metat_sr: SAMN18797630, and metag_lr: SAMN18797631).
Metaproteomics data of the GDB sample is available at ProteomeXchange under accession PXD025505.
The code used for the analysis is available at https://doi.org/10.6084/m9.figshare.14447553 and supplementary data of relevant results is available at https://doi.org/10.6084/m9.figshare.14447559.
Note: For metaP data access, see also `notes/gdb_metap.md`.
## Conda and snakemake
Install `conda` and create the main `snakemake` environment (see `README.md`).
## Other tools
Clone `OPERA-MS` repository
```bash
# in the code directory
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# Access for submitted metaP data
Credentials required for data access as long as the submission is not public:
**ProteomeXchange accession**: PXD025505
**Username**: reviewer_pxd025505@ebi.ac.uk
**Password**: tj66CIfK
The submission includes the raw proteomic data, the spectra data and identifications files for each analyzed protein FASTA file.
# Code
Code used to generate metaP reports which are included in the report workflow.
The reports were generated for
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