STAR 2.7.9a --- 2021/05/05 ::: STARsolo: multi-gene reads

[alexdobin]

Major updates:

• STARsolo can perform counting of multi-gene (multi-mapping) reads with --soloMultiMappers EM [Uniform Rescue PropUnqiue] options.
• PR simple, but inelegant support for non-x86 using SIMDe #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 SOURCE_DATE_EPOCH to make the build more reproducible #1164: SOURCE_DATE_EPOCH to make the build more reproducible
• PR Show which STAR binary+version is executed #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 Also cleaning opal/opal.o #1156: clean opal/opal.o
• Issue Segmentation Fault When STARSolo Starts Counting #1166: seg-fault for STARsolo --soloCBwhitelist None (no whitelist) with barcodes longer than 16b
• Issue STARSolo CR/UR scrambled in TranscriptomeSAM #1167: STARsolo CR/UR SAM tags are scrambled in TranscriptomeSAM file Aligned.toTranscriptome.out.bam. This bug appeared in 2.7.7a.
• Issue PCR duplicates issue when WASP tag included #1177: Added file checks for the --inputBAMfile .
• Issue Wrong NH tag when outSAMmultNmax flag is set to 1 #1180: Output the actual number of alignments in NH attributes even if --outSAMmultNmax is set to a smaller value.
• Issue Output of GX/GN in non-solo runs #1190: Allow GX/GN output for non-STARsolo runs.
• Issue 2.7.8a 2-pass produces corrupt SAM #1220: corrupt SAM/BAM files for --outFilterType BySJout. The bug was introduced with the chnages in 2.7.7a.
• Issue Seemingly unrelated CB: in solo for DropSeq #1211: scrambled CB tags in BAM output for --soloCBwhitelist None --soloFeatures Gene GeneFull.
• Fixed a bug causing seg-faults with --clipAdapterType CellRanger4 option.

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This discussion was created from the release STAR 2.7.9a --- 2021/05/05 ::: STARsolo: multi-gene reads.

[alexdobin]

STARsolo manuscript is out on bioRxiv:
https://www.biorxiv.org/content/10.1101/2021.05.05.442755v1