CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[rc1.0.5] - 2022-06-02

Added

STAR Alignment

• V&V implemented akin to RSEM counts table
  • Ensure counts correctly aggregated from {sample}_ReadsPerGene.out.tab

Changed

RSEM Index naming

• Uses {Oorg}.grp for file prefix (e.g. Mmus.grp / Mmus_ERCC.grp)

RSEM Count

• Unnormalized_Counts.csv renamed to RSEM_Unnormalized_Counts.csv to disambiguate compared to STAR_Unnormalized_Counts.csv

Staging

• raw fastq.gz files will now be named as they were originally named in the GLDS repo
  • Files derived from those original raw fastq.gz will be renamed to a standard format (as opposed to renaming the original raw files in a standard format)

Fixed

DESEQ2 Annotations

• Modified to use database files generated in-house.
  • This addresses a bug in STRINGdb and may be reverted once the STRINGdb bug fix is released

Post Processing

• md5sum table is not synced with assay table
  • Now correctly synced

[rc1.0.4] - 2022-06-02

STAR Alignment

Added

• New published files
  • Output directory: 02-STAR_Alignment
    • STAR_NumNonZeroGenes.csv
      • A dataset wide tabulation of the number of genes with non zero counts.
    • STAR_Unnormalized_Counts.csv
      • A dataset wide tabulation of gene counts output from STAR.

Fixed

• STAR_Unnormalized_Counts.csv file is published as originally intended

[rc1.0.3] - 2022-04-30

Added

STAR Alignment

• Will now output quantification 'GeneCounts' (in addition to TranscriptomeSAM)

Changed

Fixed

Removed

0.1.1-beta - 2022-03-09

Fixed

• Python scripts set to executable

[0.1.0-beta] - 2022-01-21