RetroMiner to RTPEA

Steps to retrieve data from RetroMiner and populate into MongoDB for RTPEA

RetroMiner

The last script of RetroMiner is "Data_filtering.sh", which uses a custom version of PeptideShakers' ReportCLI to write out tables with the protein identification information we need for all proteins

Get RT data out - create_results_table.sh (working)

Apocrita

sh custom_report2.sh

this script runs the modified data export for PeptideShaker and outputs .txt files loop requires a list of PXDs in a text file. write a way to automatically find the ones not parsed. (maybe using reanalysis log)

run second part of the script for the filtration awk commands filter RT protein lines out super fast and create LINE and HERV .txt files

Create output table

Apocrita

creates one output table with all results

Rscript parser_argumented.R --PXD "PXD00xxxx"

makes new folder called final move all filtered files into final folder

collate output table

Apocrita

Rscript make_output_table.R

visualise results

Apocrita

Rscript result_interpretation.R

Table Data

DropBox

Table data

/data/results/

add metadata

DropBox

Rscript adding_consequence_to_output_table.R

convert results to json

DropBox

using example.json

Rscript convert_results_to_json_working_final.R

move all json files to new folder and put this script in there

python Fix_Json_ORF.py

move them out of the newly generated folder back out and delete generated folder

ProtVista data

DropBox

/variants/

using visualise_example_new.json

Rscript conversion_4.R

need to add a newly compiled PXD list

merge into one file per protein

Apocrita

/ProtVista/results/

sh combine_protvista_json_files.sh

ideogram data

DropBox

in data/variants/

using sequences from data/variants/sequences

Rscript ideogram.R

bar chart data

Apocrita

on Apocrita /outputs/

du -sh *

use this to write all files into one file and call it sizes.txt

move to dropbox

make a matrix with sizes and PXDs

Rscript sizes.R