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2.7.0e bug fix release for STARsolo: single cell RNA-seq mapping, demultiplexing and gene quantification.Latest release
STAR 2.7.0e 2019/02/25
- This is a bug fix release replacing 2.7.0a,b,c,d
- Fixed problems with --quantMode GeneCounts and --parametersFiles options
STAR 2.6.1d 2018/11/16
- Fixed the problem causing BAM sorting error with large number of threads and small ulimit -n (github.com//issues/512).
- Fixed the bug causing inconsistent output for mate1/2 in the Unmapped files (github.com//issues/222).
- Fixed the non-thread safe error/exit (github.com//issues/514), and non-safe file size check (github.com//issues/516)
- Many thanks to Paul Menzel for helping to track and fix these problems.
STAR 2.6.1a 2018/08/14
- Process substitution can now be used with zipped VCF files, e.g. --varVCFfile <(zcat vcf.gz)
- Implemented fatal error exception if no SNPs are found in VCF files.
- Implemented --chimOutJunctionFormat 1 option to output some metadata (command lines and basic mapping statistics) at the end of Chimeric.out.junction file.
- The default value of --peOverlapMMp is reduced to 0.01 for less aggressive mate merging.
- Fixed the problem with control characters (ASCII<32) in genome and input read sequences. They used to be converted to N, now they are removed.
- Fixed a bug that caused serious problems with --sjdbInsertSave All option.
- Fixed a bug in merging mates (--peOverlap*) algorithm that was causing rare seg-faults.
- Fixed the GtstrandBit problem.
- Fixed a bug with multiple RG lines when inputting reads in SAM format.
- Fixed a bug causing seg-faults with shared memory and --outStd options.
- Fixed a bug with --outTmpDir and fifo files.
STAR 2.6.0c 2018/05/10
- Fixed bugs in merging mates (--peOverlap*) and WASP filtering algorithms. Please see CHANGES and RELEASEnotes from 2.6.0a below.
STAR 2.6.0b 2018/05/02
- Fixed bugs introduced in 2.6.0a. Please see CHANGES and RELEASEnotes from 2.6.0a below.
STAR 2.6.0a 2018/04/23
Major new features:
- Merging and mapping of overlapping paired-end reads with new options --peOverlapNbasesMin and --peOverlapMMp. The developmment of this algorithm was supported by Illumina, Inc. Many thanks to June Snedecor, Xiao Chen, and Felix Schlesinger for their extensive help in developing this feature.
- --varVCFfile option to input variant VCF file.
- New SAM attributes in the --outSAMattributes, vG, vA, and vW to report variants overlapping alignments.
- --waspOutputMode option for filtering allele specific alignments. This is re-implementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker, Yoav Gilad & Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12, 1061–1063 (2015), https://www.nature.com/articles/nmeth.3582 . Many thanks to Bryce van de Geijn for fruitful discussions.
- Detection of multimapping chimeras, with new options --chimMultimapNmax, --chimMultimapScoreRange and --chimNonchimScoreDropMin . Many thanks to Brian Haas for testing and feedback.
Minor new features:
- --alignInsertionFlush option which defines how to flush ambiguous insertion positions: None: old method, insertions are not flushed; Right: insertions are flushed to the right.
- --outSAMtlen option to select the calculation method for the TLEN field in the SAM/BAM files.
- --outBAMsortingBinsN option to control the number of sorting bins. Increasing this number reduces the amount of RAM required for sorting.