STAR 2.7.4a ______ 2020/06/01

Fixed multiple bugs and issues.

This version requires re-generation of the genome indexes

• Fixed the long-standing seg-fault problem for small genomes.
• Issue #784: Fixed a seg-fault in STARsolo for cases where no cell barcodes matched whitelist.
• Issue #798: Fixed the problem in Solo Q30 Bases in Summary.csv average (#798).
• Issue #843, #880: Throw an error if read file in --readFilesIn does not exist when using --readFilesCommand .
• Issue #864: Fixed seg-fault for STARsolo runs with very small number of reads or cells.
• Issue #881: Check if --genomeDir exists, create if necessary.
• Issue #882: Added 3rd column "Gene Expression" to solo features.tsv file for better compatibility with downstream tools.
• Issue #902: Fixed seg-fault for STARsolo CB/UB SAM attributes output with --soloFeatures GeneFull only option.
• Issue #907: Fixed the bug that prevented output of STARsolo GX/GN tags into the Aligned.out.bam if --quantMode TranscriptomeSAM is used.
• Issue #910: The output directory in --outFileNamePrefix is checked and created if it does not exist.
• If solo barcode read length is not checked (--soloBarcodeReadLength 0) and it is shorter than CB+UMI length, the barcode is padded with Ns and not counted.
• For genome generation runs, the Log.out file is moved into the --genomeDir directory.
• Fixed a bug with solo SJ output for large genomes.
• Implemented --seedMapMin option (previously hard-coded) to define minimum seed length.

STAR 2.7.3a ______ 2019/10/08

Major new STARsolo features:

• Output enhancements:
  • Summary.csv statistics output for raw and filtered cells useful for quick run quality assessment.
  • --soloCellFilter option for basic filtering of the cells, similar to the methods used by CellRanger 2.2.x.
• Better compatibility with CellRanger 3.x.x:
  • --soloUMIfiltering MultiGeneUMI option introduced in CellRanger 3.x.x for filtering UMI collisions between different genes.
  • --soloCBmatchWLtype 1MM_multi_pseudocounts option, introduced in CellRanger 3.x.x, which slightly changes the posterior probability calculation for CB with 1 mismatch.
• Velocyto spliced/unspliced/ambiguous quantification:
  • --soloFeatures Velocyto option to produce Spliced, Unspliced, and Ambiguous counts similar to the velocyto.py tool developed by LaManno et al. This option is under active development and the results may change in the future versions.
• Support for complex barcodes, e.g. inDrop:
  • Complex barcodes in STARsolo with --soloType CB_UMI_Complex, --soloCBmatchWLtype --soloAdapterSequence, --soloAdapterMismatchesNmax, --soloCBposition,--soloUMIposition
• BAM tags:
  • CB/UB for corrected CellBarcode/UMI
  • GX/GN for gene ID/name
• STARsolo most up-to-date documentation.

2.7.2d 2019/10/04 bug-fix for Chimeric.out.sam

• Fixed the problem with no header in Chimeric.out.sam

2.7.2b

STAR 2.7.2b 2019/08/29

Bug fixes in chimeric detection, contributed by Meng Xiao He (@mengxiao)

• Fix memory leak in handling chimeric multimappers: #721
• Ensure chimeric alignment score requirements are consistently checked: #722,#723.

2.7.2a: chimeric detection improvements

STAR 2.7.2a 2019/08/13

Major improvements in chimeric detection, contributed by Brian Haas @brianjohnhaas:

• Chimeric read reporting now requires that the chimeric read alignment score higher than the alternative non-chimeric alignment to the reference genome. The Chimeric.out.junction file now includes the scores of the chimeric alignments and non-chimeric alternative alignments, in addition to the PEmerged bool attribute.

Big fixes and minor features:

• Fixed the problem with ALT=* in STAR-WASP.
• Implemented extras/scripts/soloBasicCellFilter.awk script to perform basic filtering of the STARsolo count matrices.

2.7.1a new STARsolo features and bug fixes

STAR 2.7.1a 2019/05/15

This version requires re-generation of the genome indexes

• Implemented --soloFeatures GeneFull which counts reads overlapping full genes, i.e. includes reads that overlap introns. This can be combined with other features, e.g. --soloFeatures Gene SJ GeneFull .
• Implemented --soloCBwhitelist None option for solo* demultiplexing without CB whitelist. In this case error correction for CBs is not performed.
• Implemented Cell Barcodes longer than 16 bases (but shorter than 31 bases). Many thanks to Gert Hulselmans for implementing this feature (#588).
• Implemented collapsing of duplicate cell barcodes in the whitelist.
• Implemented --sjdbGTFtagExonParentGeneName and --sjdbGTFtagExonParentGeneType options to load gene name and biotype attributes from the GTF file.
• Fixed problems created by missing gene/transcript ID, name and biotype attributes in GTF files (issues #613, #628).
• Added warning for incorrectly scaled --genomeSAindexNbases parameter (issue #614).
• Added numbers of unmapped reads to the Log.final.out file (pull #622).
• Fixed a problem which may cause seg-faults for reads with many blocks (issue #342).

STARsolo 2.7.0f bug fix release

STARsolo: 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.
• Requires re-generation of the genome index.
• Compiled with gcc-5.3.0, and requires at least gcc-4.9.4

STAR 2.7.0f 2019/03/28

• Bug fix release replacing 2.7.0a,b,c,d,e
• Fixed a problem in STARsolo with empty Unmapped.out.mate2 file. Issue #593.
• Fixed a problem with CR CY UR UQ SAM tags in solo output. Issue #593.
• Fixed problems with STARsolo and 2-pass.

STAR 2.7.0e 2019/02/25

• Fixed problems with --quantMode GeneCounts and --parametersFiles options

STAR 2.7.0d 2019/02/19

• Implemented --soloBarcodeReadLength option for barcode read length not equal to the UMI+CB length
• Enforced genome version rules for 2.7.0

STAR 2.7.0c 2019/02/08

• This release is compiled with gcc-4.8.5, and requires at least gcc-4.8.5
• Fixed another problem in STARsolo genes.tsv output.
• Replaced tabs with spaces in STARsolo matrix.mtx output
• #559, #562 Fixed compilation problems.
• #550 (again, previous merge failed): Added correct header for the STARsolo matrix.mtx file, needed for python scipy mmread compatibility.

STAR 2.7.0b 2019/02/05

• #550: Added correct header for the STARsolo matrix.mtx file, needed for python scipy mmread compatibility.
• #556: Fixed a problem with STARsolo genes.tsv file, which may also cause troubles with GTF files processing.
• Important: 2.7.0x releases require re-generation of the genome index.

STAR 2.7.0a 2019/01/23

• 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.
• This release is compiled with gcc-5.3.0, and requires at least gcc-4.9.4

2.7.0e bug fix release for STARsolo: single cell RNA-seq mapping, demultiplexing and gene quantification.

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.

2.6.1e: bug fix patch on 2.6.1 branch.

STAR 2.6.1e 2019/07/25

• Fixed a bug causing rare seg-faults with for --peOverlap* options and chimeric detection.

2.6.1d bug fix 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.