Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/databio/ppqc

QC samples for PEPPRO pipeline

https://github.com/databio/ppqc

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

QC samples for PEPPRO pipeline

Basic Info
  • Host: GitHub
  • Owner: databio
  • Default Branch: master
  • Homepage:
  • Size: 83 KB
Statistics
  • Stars: 1
  • Watchers: 14
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created almost 7 years ago · Last pushed almost 4 years ago
Metadata Files
Readme

README.md

Peppro QC PEP

Get source samples using geofetch

geofetch -i sra_accessions.txt -n ppqc

Grab the source sample metadata here:

wget -r http://big.databio.org/peppro/sra_meta/ppqc/ .

Get RNA-seq spike-in samples here:

wget http://big.databio.org/peppro/fastq/K562_[1-9]0pct_RNArc_r2.fastq.gz .

Validate the configuration file with eido like so:

eido -p peppro_paper.yaml -s http://schema.databio.org/pipelines/ProseqPEP.yaml

Create user-specific environment variables

  • $CODE: this is a path to the parent directory where scripts and code are stored
    • For example:CODE=/scratch/userid/src/
  • $DATA: this is a path to the parent directory where input files are stored
    • For example:DATA=/project/shefflab/data/
  • $PROCESSED: this is a path to the parent directory to where output should be written
    • For example:PROCESSED=/project/shefflab/processed/

Run in looper:

looper run ppqc/peppro_paper.yaml

The peppro_paper.yaml file is the working PEP for these samples. The peppro_paper.csv file is the working annotation file for these samples.

Owner

  • Name: Databio
  • Login: databio
  • Kind: organization
  • Location: University of Virginia

Solving problems in computational biology

GitHub Events

Total
Last Year

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 2
  • Total pull requests: 0
  • Average time to close issues: 2 months
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 3.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nsheff (2)
Pull Request Authors
Top Labels
Issue Labels
docs (1)
Pull Request Labels