Releases: cancerit/cgpRna
v2.0.13 - Grass annotation script added
Merge tag '2.0.13' into dev adding script to add grass flag to fusion output
v2.0.12 - Bugfix: compare overlapping fusions - chromosome names
Removing chr from the start of each line in the filtered GTF files used by the comparison script so that the bedtools closest command works correctly.
The Tophat-fusion, star and deFuse output doesn't have chr in the chromosome names so the GTF file needs to be comparable.
v2.0.11 - changes to setup.sh
- Update to shebang line in defuse perl scripts to use version of Perl on PATH
- Multi threading make commands to increase speed of installation
v2.0.10 - Bugfix - defuse.pl should be run by environment version of Perl
Merge tag '2.0.10' into dev Ensuring that defuse.pl is run using Environment version of Perl
v2.0.9
v2.0.8 - changes for latest version of Tophat
Merge tag '2.0.8' into dev Changes for latest Tophat release
v2.0.7 - Latest updates to fusion pipeline
- Changing ref data set-up for TopHat
- Updated README
v2.0.6 - Bugfix: Using STAR parameter --outSAMheaderHD to add SO tag into header line
The final stage in the star mapping code is to coordinate sort the aligned BAM file using biobambam bamsort.
This should update the @hd header line with the following tag SO:coordinate but this was not happening becuase STAR does not add the SO tag by default. It should be adding SO:unsorted to the output mapped BAM.
Now the STAR parameter --outSAMheaderHD is used to ensure the SO tag is present prior to sorting with bamsort.
v2.0.5 - Bugfix: renaming GeneCoverage file produced by RSeQC
process_qcstats.pl checks that the RSeQC output files have been successfully produced. The gene coverage output file names have changed from .coverage.geneBodyCoverage.* to .geneBodyCoverage.*
Have updated the gene_coverage subroutine RnaQC/Implement.pm to reflect this
v2.0.4 - Bugfix to ensure ID is listed as first RG tag
Merge tag '2.0.4' into dev Bugfix to ensure ID is always listed first for the RG line