Skip to content

Releases: epigen/genome_tracks

v1.0.1 - stable version with complete docs and DOI

21 Mar 13:20
@sreichl sreichl
v1.0.1
1ee59ed
Compare
Choose a tag to compare
v1.0.1 - stable version with complete docs and DOI Latest
Latest

v1.0.1 - stable version with complete docs and DOI

Documentation

  • Add Zenodo DOI

v1.0.0 - stable version with complete docs

Features

  • Processing
    • (optional) Single-cell BAM file splitting into groups based on metadata.
    • Merging and indexing of BAM files by group.
    • Generation of bigWig files for merged BAM files.
    • Extraction and extension of gene coordinates from 12-column BED files.
    • Creation of a BED file for all genes and genomic regions for IGV-report.
  • Visualization
    • Generation of customized plots for each gene/genomic region including all groups.
    • Creation of an interactive self-contained IGV-report for merged BAM files.
    • Setup of a UCSC genome browser track hub for all bigWigs, with color coding.

Documentation

  • Usage Recommendations and advice for efficient workflow execution.
  • Runtime information for ATAC-seq, RNA-seq, and scRNA-seq samples.
  • Genome Browser Tracks: Instructions for using the UCSC Genome Browser Track Hub and IGV for visualization.
  • Resources: Recommendations for compatible MR.PARETO modules and UCSC Genome Browser annotation track database

Full Changelog: v0.1.0...v1.0.0

Assets 2

v1.0.0 - stable version with complete docs

21 Mar 13:09
@sreichl sreichl
v1.0.0
d0e4676
Compare
Choose a tag to compare
v1.0.0 - stable version with complete docs

Features

  • Processing
    • (optional) Single-cell BAM file splitting into groups based on metadata.
    • Merging and indexing of BAM files by group.
    • Generation of bigWig files for merged BAM files.
    • Extraction and extension of gene coordinates from 12-column BED files.
    • Creation of a BED file for all genes and genomic regions for IGV-report.
  • Visualization
    • Generation of customized plots for each gene/genomic region including all groups.
    • Creation of an interactive self-contained IGV-report for merged BAM files.
    • Setup of a UCSC genome browser track hub for all bigWigs, with color coding.

Documentation

  • Usage Recommendations and advice for efficient workflow execution.
  • Runtime information for ATAC-seq, RNA-seq, and scRNA-seq samples.
  • Genome Browser Tracks: Instructions for using the UCSC Genome Browser Track Hub and IGV for visualization.
  • Resources: Recommendations for compatible MR.PARETO modules and UCSC Genome Browser annotation track database

Full Changelog: v0.1.0...v1.0.0

Assets 2

v0.1.0 - stable version with complete docs

15 Jan 13:23
@sreichl sreichl
v0.1.0
70c6c93
Compare
Choose a tag to compare
v0.1.0 - stable version with complete docs

A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files powered by the wrapper gtracks for the package pyGenomeTracks.

features

  • processing
    • BAM files of the same group are merged and indexed using samtools.
    • A bigWig file per merged BAM file is generated using deepTools::bamCoverage.
    • Information per requested gene from the 12-column BED file is retrieved (not necessary for genomic regions).
    • coordinates from the 12-column BED file are extracted and extended at the start and end by the configured parameter.
    • the number of isoforms i.e. number of lines in the BED file is determined (only for genes, for genomic regions it is hardcoded to 1) to plot below the tracks.
  • visualization
    • generate one plot per category of bigWigs and gene/region with the determined gene parameters.
    • generate one plot including ALL categories per gene/region.

documentation

  • complete documentation of used software, all features, and methods
  • external resources
Assets 2