RNA-SeQC 2.2.2

Bug Fixes:

• Fixed an exon-ordering bug which inflated CV values

RNA-SeQC 2.2.1

New Features:

• Added Chimeric Alignment Rate metric

Bug Fixes:

• Removed some debug code that was accidentally left in

RNA-SeQC 2.2.0

New Features:

• Added a new gene_fragments.gct output file which counts the unique number of fragments (not reads) for each gene

Bug Fixes:

• Fixed an issue with 3' bias being inaccurately modeled
• Fixed a few typos

Other Changes:

• Added an error message in plot.py when attempting to plot only one sample

RNA-SeQC 2.1.2

Bug Fixes:

• Fixed an issue with 3' Bias calculation that resulted in overly-extreme bias

Other Changes:

• Changed the formula for Mapping Rate:
  • Previous formula: Read Mapped (!0x4) / All Reads
  • New formula: Read Mapped (!0x4) / Primary Read (! (0x100 || 0x200))

RNA-SeQC 2.1.1

Deleted Features

• Removed the --split-distance argument. This was only useful in legacy mode. Split distance is now hard-coded to 100bp. The "Split Reads" metrics field is only reported in legacy mode

Bug Fixes:

• Fixed --fasta argument not having any effect. Previously crams were entirely parsed using your computer's htslib cache. Now, if a fasta is provided, it will be used in place of the cache

RNA-SeQC 2.1.0

New Features:

• Added experimental support for CRAM files. Use the --fasta option to provide a reference fasta to parse the input cram

Other Changes:

• Renamed "Disqualified Reads" and "Disqualification Rate" to "Ambiguous Alignment Rate"
• Low Quality reads are now included in Intron/Exon statistics, however, they are not included in computing any readcounts or coverage. To get a count of High-Quality only "Exonic" reads, check the new "High Quality Exonic Rate".
• Added "High Quality" versions of "Exonic Rate", "Intronic Rate", "Intergenic Rate", "Intragenic Rate", and "Ambiguous Alignment Rate".
• Renamed "Low Quality Reads" to "Low Mapping Quality Reads". "Low Quality Reads" now refers to reads with more than 6 mismatches, a non-perfect mapping quality, or which are not properly paired.

Bug Fixes:

• Fixed exonic rate reported in --legacy mode

RNA-SeQC 2.0.0

Total rewrite of RNA-SeQC 1.1.9

• Added 18 new QC metrics
• Vastly improved memory usage
• Improved runtime
• Enhanced depth-of-coverage metrics
• Added fragment length calculations and statistics
• Minor bugfixes to improve accuracy of gene and exon readcounts