Version 0.0.8

• Replaced htseq-count with GenomicAlignments::summarizeOverlaps

  • Now it is faster to count reads
  • The configuration of read counting step is moved to settings.yaml file under
    a new section: "counting"

• star_map and star_index configuration is now split into two (#55)

• sorting of BAM files is now done using samtools sort (replaced sorting by STAR) (#51)

Version 0.0.7

New Features

• replaced counts from STAR with ht-seq counts (fixes issue #34 about strandedness)
  • now it is possible to configure counting modes, strandedness, feature types,
    file formats and any other configuration possible using htseq-count.
• reorganized counts folder
  • redirect all count tables (from htseq-count or salmon or star) to a
    common folder ("feature_counts").
• creates normalized counts table for all samples using deseq2::estimateSizeFactors
• Genome coverage (bigwig files) is now normalized using deseq2 size factors.

Fixes issue #34

Version 0.0.6

Replaced bedgraph with strand-specific bigwig files for genome coverage.

Fixed bug related to STAR version 2.7.0

Updated instructions for Conda environments.

Fixed issue #52

Version 0.0.5

• Fixed build with Snakemake 5
• Fixed bug #43
• Fixed bug #44

Version 0.0.4

pigx_rnaseq-0.0.4.tar.gz

Version 0.0.3.

v0.0.3

Version 0.0.3.

Version 0.0.2

v0.0.2

Release 0.0.2.