RNA-SeQC 2.4.2

Bug Fixes:

• Fixed an issue preventing GC content statistics from being generated
• Fixed a long standing issue with --fasta references and crams (#50)

Other Changes:

• Bumped the rnaseqc python module to version 0.0.3
• Improved unit tests
• Added tests for, and warnings regarding cram/reference mismatches. htslib is a nightmare

RNA-SeQC 2.4.1r1

Bug Fixes:

• Fixed a crash when collecting GC statistics for some bams
• Fixed a syntax error present in the original 2.4.1 release

RNA-SeQC 2.4.0

New Features:

• Added GC-Content metrics when a fasta is provided with --fasta:
  • A new .gc_content.tsv file is generated with read counts binned by gc content fraction
  • .metrics.tsv file now reports mean, standard deviation, skew, and kurtosis of GC content distribution
• Added new .exon_cv.tsv file which reports exon CV and GC Content

RNA-SeQC 2.3.6

New Features:

• Added new python scripts to the python/ directory. These scripts are useful for viewing and aggregating RNA-SeQC results
  • The python code is now distributed on pip! Install with pip install rnaseqc or (from the cloned repo) pip install -e python
  • The python code has moved in the docker image. Run utilities inside the image with python3 -m rnaseqc

Bug Fixes:

• Fixed a bug which caused too much leniency when selecting reads for the insert size distribution
• Fixed a bug which allowed for genes shorter than the coverage mask to be counted as having 0 coverage
• Chimeric Alignment Rate now uses the correct numerator
• Fixed a bug in median calculation
• Fixed a bug in fragment size statistics

Other changes:

• Removed the Reads excluded from exon counts metric. This stopped being used a while ago but was still reported (at 0)
• Removed the Duplicate Reads metric. It has no practical difference to Mapped Duplicate Reads

RNA-SeQC 2.3.5

Bug Fixes:

• Reworded the documentation for --unpaired. It is required for single end libraries
• Fixed a bug in the duplicate feature detection during GTF loading

RNA-SeQC 2.3.4

Bug Fixes:

• Fixed impossibly small fragments from being counted in the fragment size distribution

New Features:

• You can now provide date and cohort annotations to the plotting code, which will color and sort the samples in your figures

RNA-SeQC 2.3.3

New Features:

• Added Non-Globin duplication metrics, which compute duplication rate excluding reads which aligned to Globin genes

Other Changes:

• Updated SeqLib to latest
• Expression Profiling Efficiency changed to match old behavior which was a better measure. Current formula is Exonic Reads / Unique Mapping, Vendor QC Passed Reads
• When running in --unpaired mode, the sense rate is reported as End 1 Sense Rate, this now matches the behavior of other End 1/2 metrics

RNA-SeQC 2.3.2

Bug Fixes:

• Fixed rare crash when given duplicated gene/exon ids (#26)

RNA-SeQC 2.3.1

Bug Fixes:

• Fixed --stranded flag behaving unexpectedly (#25)

RNA-SeQC 2.3.0

Other Changes:

• Changed how 3' bias is calculated:
  • Only genes with a median coverage of 100 within 50 bases of their coverage peak will be considered
    • The threshold cannot be changed, but that window is equal to the size of --window-size
  • Drop coverage on both ends of genes until a base is encountered which is in the 6th percentile *(or above) of coverage for that gene
• Bias is based on the median expression at the (trimmed) ends of the gene instead of the mean