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
......@@ -4,8 +4,20 @@ Notes for those trying to reproduce the results from the publication.
# 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 and supplementary data of relevant results is available at
Note: For metaP data access, see also `notes/`.
## Conda and snakemake
Install `conda` and create the main `snakemake` environment (see ``).
## Other tools
Clone `OPERA-MS` repository
# in the code directory
# Access for submitted metaP data
Credentials required for data access as long as the submission is not public:
**ProteomeXchange accession**: PXD025505
**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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