Version 2.2.3

Changes

• Fix Docker/Singularity container to properly install locfit module required for DESeq2 (Issue #120)
• Many thanks to @molikd for the patch.

Version 2.2.2

Changes

• Provided support for Docker/Singularity
  • Many thanks to @molikd for this update.

Minor changes

• Added parameter --outdir to allow specification of output directory (#117)
  • The output directory must already exist
• Updated argparse requirement as it is now a standard Python library (#111)
• Enable independent filtering by default in DESeq2 script (#114)

Zenodo release

• No changes from version 2.2.1

Version 2.2.1

Minor fix

• Allow --verbose to be invoked without arguments

Version 2.2.0

Changes

• Added Python 3 compatibility (as requested by issue #61)

Minor changes

• Minor fixes to read apportioning
• Minor fixes to correctly handle SAM as input
• Minor fixes to features list when running on unstranded libraries

Version 2.1.4

Changes

• Updated the --stranded parameter to utilize forward instead of yes for stranded libraries sequenced in the direction of transcribed RNA.
• Clarified library prep that would utilize --stranded forward parameter
  • Thanks to Kimberley Billingsley for spotting the mistake.

Version 2.1.3

Changes

• Added the ability to accept pre-built TE (or gene) GTF indices. This will save time when the same index is used by multiple runs. Pre-built TE GTF indices for human and mouse are available here. Please decompress (gunzip) before use.
  • Many thanks to Talitha (@talithaforcier) for the implementation, and lexa for the suggestion.

Minor changes

• R package loading messages now suppressed when running TEtranscripts.
• Minor update on help message for --stranded parameter.
• Fixed errors introduced during repository merge.

Version 2.0.5

Changes

• --stranded now defaults to no
• Improved explanation of --stranded option in README and help message

Version 2.0.4

Rebranding

• Tool package has been renamed to TEtranscripts.

Minor changes

• Fixes to R code for differential analysis
• Comment lines now handled properly in GTF file (issue #36)

Version 2.0.3

Minor fixes

• Changed DESeq2 results() parameter from alpha=1.0 to independentFiltering=F to prevent crashing when using newer versions of DESeq2