v1.1.1

• Fixed some issues in the installation procedure caused by new version of dependency Python packages no more supporting Python2.7
• Installation now supports virtualenv
• Updated to SCons 3.1.2
• Updated to CIRCexplorer2 v2.3.8
• Updated StringTie to v2.1.1
• Removed support for Fastx-toolkit

v1.1

• fixed bug that caused CIRCexplorer2-segemehl to underestimate circrna read counts
• fixed error when single method is used
• fixed index-to-build check for dcc and circrna_finder
• use a python script to convert circRNA GTF into start-stop GTF it instead of shell commands

v1.0

We have been using CirComPara enough to exit the 'developing' tags and finally we now issue the 'production' version, which considers:

• a make_circrna_html script to merge results from different CirComPara directories/analyses
• updated installation script to new versions of dependency programs
• more robust generation of genePred annotation file
• improved gene annotation and strand assignement for circRNAs
• improved automatic parameter setting for stranded library in single-end mode
• now when transcriptome reconstruction is enabled, the new transcriptome is used in circRNA detection
• various bugfixes

v0.6.1a

• Fixed errors when using multiple linear expression and differential expression methods
• Added option CIRC_DIFF_EXP to enable circRNA differential expression reporting
• Minor bugfixes

v0.6.0

Included two new circRNA detection methods:

• DCC
• circRNA_finder

Dismissed computation of correlation to linear gene expression in favor of circular-to-linear expression ratio computed as in DCC

CircRNA expression is no more represented as RPMs but as the median of circRNA methods' raw counts

Improved annotation of circRNA strand and host-gene

Updated packages' version:

• Trimmomatic v0.38
• CIRCexplorer2 v2.3.3
• Segemehl v0.3.2
• STAR v2.6.1d

Added new options to better control programs used in the pipeline:

• TESTREALIGN_PARAMS to filter segemehl results (the testrealign script is no more present from segemehl v0.3, but the name is left here)
• LIN_COUNTER to use CirComPara's (ccp) or DCC linear expression corresponding to backsplices
• SAM_SORT_MM to set samtools memory usage
• FIX_READ_HEADER to clean FASTQ read ids before circRNA alignments (can be useful when analyzing SRA readsets)
• UNSTRANDED_CIRCS to force unstrandness of detections

Improved task dependencies to speed up parallel computing

v0.3.0-beta

• StringTie is now the default linear expression program
• added support of Ballgown
• updated Trimmomatic to v0.38
• added possibility of bypassing circRNA prediction and runonly the linear part
• added computation of GC content
• removed default -C and -T parameters for segemehl mapping
• fixed error in labelling as intergenic some cases of intronic circRNAs and annotation now refers only to backsplice sites instead of the whole region of backsplice overlap
• fixed color error when > 5 samples in one condition
• fixed error for non literal chars in sample names
• various code fixes

v0.2.2

Minor bugfixes

v0.2.0

NEW FEATURES:

• new circRNA methods added thanks to the update to CIRCexplorer2 (CIRCexplorer v1 has been replaced by circexplorer_star in CIRCRNA_METHODS; ). Now CirComPara supports:
  • CIRCexplorer2 on BWA (circexplorer_bwa),
  • CIRCexplorer2 on STAR (circexplorer_star),
  • CIRCexplorer2 on Segemehl (circexplorer_segemehl),
  • CIRCexplorer2 on TopHat2 (circexplorer_tophat).
• Added option BYPASS_LINEAR to bypass linear expression analysis and run only circRNA methods (could be useful for Circle-seq).
• use of the make_indexes utility is now documented in README

BUGFIXES:

• The adapter column is no more required in META file;
• The CIRI parameter is no more required;
• Fixed log2(fold_change) column values in Cuffdiff processed result table DEG_tests_by_contrast.csv to make them consistent with the 'A vs B' notation: in gene_exp.diff file, instead, Cuffdiff reports fold changes of 'sample_2 vs sample_1';
• Fixed potential error for representation of BED coordinates

v0.1.3

Updates:

• fixed dependency cycle when using pre-built indexes;
• fixed generated .genePred annotation when using annotation with missed gene_name tags: gene_id will be used instead

v0.1.2

Updates:

• fixed error when using single-end reads
• included meta file to test single-end read mode
• added How-to-cite section in README