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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

STARsolo

  • This release introduces STARsolo for: mapping, demultiplexing and gene quantification for single cell RNA-seq.
  • Multiple solo* options control STARsolo algorithm. See the RELEASEnotes and the manual for more information.
Assets 2

@alexdobin alexdobin released this Nov 16, 2018 · 87 commits to master since this release

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.
Assets 2

@alexdobin alexdobin released this Oct 17, 2018 · 94 commits to master since this release

STAR 2.6.1c 2018/10/17

  • Enforced the consistent choice of supplementary chimeric alignments for overlapping mates.
Assets 2

@alexdobin alexdobin released this Sep 6, 2018 · 99 commits to master since this release

STAR 2.6.1b 2018/09/06

  • Fixed a problem with --outSAMfilter KeepOnlyAddedReferences option.
  • Fixed a problem with output of an empty sorted BAM.
Assets 2

@alexdobin alexdobin released this Aug 14, 2018 · 102 commits to master since this release

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.
Assets 2

@alexdobin alexdobin released this May 10, 2018 · 115 commits to master since this release

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.
Assets 2
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