Skip to content

STAR 2.7.9a --- 2021/05/05 ::: STARsolo: multi-gene reads
Compare
Choose a tag to compare
@alexdobin alexdobin released this 05 May 14:12
· 110 commits to master since this release
2.7.9a
ac39348

Major updates:

  • STARsolo can perform counting of multi-gene (multi-mapping) reads with --soloMultiMappers EM [Uniform Rescue PropUnqiue] options.
  • PR #1163: SIMDe takes care of correct SIMD extensions based on -m g++ flag: compilation option CXXFLAGS_SIMD is preset to -mavx2, but can be to the desired target architecture. Many thanks to Michael R. Crusoe @mr-c, Evan Nemerson @nemequ and Steffen Möller @smoe !

New options and features:

  • New option: --soloUMIfiltering MultiGeneUMI_All to filter out all UMIs mapping to multiple genes (for uniquely mapping reads)
  • New script extras/scripts/calcUMIperCell.awk to calculate total number of UMIs per cell and filtering status from STARsolo matrix.mtx
  • New option: --outSJtype None to omit outputting splice junctions to SJ.out.tab
  • Simple script to convert BED spliced junctions (SJ.out.tab) to BED12 for UCSC display: extras/scripts/sjBED12.awk
  • PR #1164: SOURCE_DATE_EPOCH to make the build more reproducible
  • PR #1157: print STAR command line and version information to stdout

Changes in behavior:

  • Minor changes to statistics output (Features.csv and Summary.csv) to accomodate multimappers.
  • Modified option: ---limitIObufferSize now requires two numbers - separate sizes for input and output buffers

Bug fixes

  • PR #1156: clean opal/opal.o
  • Issue #1166: seg-fault for STARsolo --soloCBwhitelist None (no whitelist) with barcodes longer than 16b
  • Issue #1167: STARsolo CR/UR SAM tags are scrambled in TranscriptomeSAM file Aligned.toTranscriptome.out.bam. This bug appeared in 2.7.7a.
  • Issue #1177: Added file checks for the --inputBAMfile .
  • Issue #1180: Output the actual number of alignments in NH attributes even if --outSAMmultNmax is set to a smaller value.
  • Issue #1190: Allow GX/GN output for non-STARsolo runs.
  • Issue #1220: corrupt SAM/BAM files for --outFilterType BySJout. The bug was introduced with the chnages in 2.7.7a.
  • Issue #1211: scrambled CB tags in BAM output for --soloCBwhitelist None --soloFeatures Gene GeneFull.
  • Fixed a bug causing seg-faults with --clipAdapterType CellRanger4 option.
Assets 2
1 Join discussion