@a_dobin

Director of Bioinformatics @ArcInstitute Formerly: ENCODE; PI@CSHL Developer of STAR.

 Palo Alto, CA
Joined August 2012
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STARsolo preprint is out on bioRxiv: biorxiv.org/content/10.1101/… STAR release 2.7.9a: github.com/alexdobin/STAR/re… The major new feature is quantification of multi-gene (multi-mapping) reads/UMIs, which are necessary to detect expression from overlapping genes and paralogs. 1/5

STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus...

We present STARsolo , a comprehensive turnkey solution for quantifying gene expression in single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR . Using simulated data that closely...

biorxiv.org
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STARsolo agrees nearly perfectly with CellRanger, both in overall gene/cell count matrices and differential gene expression between cell clusters. Kallisto and Alevin show significant differences with CellRanger. STARsolo is ~4 times faster than CellRanger and uses less RAM. 4/5
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While pseudoalignment-to-transcriptome tools are the fastest and require the least RAM, STARsolo is the fastest among the highly accurate methods. STARsolo uses less RAM and is much faster than Kallisto-bustools for single-nucleus RNA-seq and RNA-Velocity calculations. 5/5
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Our preprint "Virtue as the mean: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses": biorxiv.org/content/10.1101/… Led by @BKaminow , collaborating with @SaraBallouz and @JesseAGillis . STARconsensus is released as 2.7.7a: github.com/alexdobin/STAR/re…

Virtue as the mean: Pan-human consensus genome significantly improves the accuracy of RNA-seq...

The Human Reference Genome serves as the foundation for modern genomic analyses. However, in its present form, it does not adequately represent the vast genetic diversity of the human population. In...

biorxiv.org
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New STAR release 2.7.5a: github.com/alexdobin/STAR/re… Major new feature: STARsolo mappin and quantification for plate- based (Smart-seq) scRNA-seq.

Release STAR 2.7.5a ______ 2020/06/16 · alexdobin/STAR

STAR 2.7.5a 2020/06/16 Major new features: Implemented STARsolo quantification for Smart-seq with --soloType SmartSeq option. Implemented --readFilesManifest option to input a list of input read f...

github.com
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We analyzed Covid-19 attack rates dependence on racial/ethnic and socioeconomic factors on the sub-county level, within Suffolk County (NYS), presently the 5th most-affected county in the US. arxiv.org/abs/2004.12175 1/2
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We confirm previous observations that minorities are disproportionately impacted by Covid-19. The minority population proportion in a community is the best predictor of the attack rate, with an alarmingly high ~4-fold attack rate increase for Black and Hispanic populations. 2/2
Happy to share our new online-first publication: Evaluation of STAR and Kallisto on Single Cell RNA-Seq Data Alignment. 🙂 We found the efficiency of Kallisto comes with the trade off on performance, slightly. #singleCell #bioinformatics 1/n g3journal.org/content/early/…
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A few word on our recent manuscript, “The transcriptional legacy of developmental stochasticity” biorxiv.org/content/10.1101/… (0/18)

The transcriptional legacy of developmental stochasticity

Genetic variation, epigenetic regulation and major environmental stimuli are key contributors to phenotypic variation, but the influence of minor perturbations or “noise” has been difficult to assess...

biorxiv.org
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The transcriptional legacy of developmental stochasticity biorxiv.org/content/10.1101/…

The transcriptional legacy of developmental stochasticity

Genetic variation, epigenetic regulation and major environmental stimuli are key contributors to phenotypic variation, but the influence of minor perturbations or “noise” has been difficult to assess...

biorxiv.org
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STARsolo poster from #gi2019 is available on f1000 Genome Informatics Conference Collection: doi.org/10.7490/f1000researc…
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This year's Genome Informatics conference at @CSHL was great! I'd like to thank the organizers of #gi2019 for the chance to talk about STARsolo-Quant: a scRNA-seq isoform abundance estimator I've been working on with @a_dobin. see my slides at: f1000research.com/slides/8-1…
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Haas, Regev and co benchmark methods for identifying fusion transcripts from RNA-seq data. De novo assembly based methods are less accurate than read mapping approaches. Part of our #benchmarking special issue genomebiology.biomedcentral.…
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STAR 2.7.3a github.com/alexdobin/STAR… Major new STARsolo features: cell filtering and QC summary; support for complex barcodes (e.g. inDrop); Velocyto counts; CB/UMI tags in BAM output; better compatibility with CellRanger 3.x.x

GitHub - alexdobin/STAR: RNA-seq aligner

RNA-seq aligner. Contribute to alexdobin/STAR development by creating an account on GitHub.

github.com
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STAR 2.7.2a: github.com/alexdobin/STAR/re… Major improvements in chimeric detection and reporting, contributed by Brian Haas @brianjhaas.

Release 2.7.2a: chimeric detection improvements · alexdobin/STAR

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 t...

github.com
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STAR 2.7.1a: github.com/alexdobin/STAR/re… New single-cell RNA-seq features implemented: counting intronic (precursor mRNA) reads, no-whitelist cell barcode demultiplexing, cell barcodes longer than 16b.

Release 2.7.1a new STARsolo features and bug fixes · alexdobin/STAR

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 int...

github.com
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Alex Dobin retweeted
Adam Siepel@asiepel6 Feb 2019
Thanks for all of the great responses to this. A few more ideas I'd like to trial-balloon (feel free to aim and shoot). 1/n
Adam Siepel@asiepel5 Feb 2019
If you have funding to support software development for computational genomics, either new development or maintenance/improvement, I'd like to know your source. I'm writing a review article about challenges in funding software development and want an accurate view.
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2.7.0a release introduces STARsolo, a turnkey solution for analyzing droplet single-cell RNA sequencing (e.g. 10X) built directly into the STAR code. It produces gene counts nearly identical to 10X CellRanger. At the same time, STARsolo is ~10 times faster than the CellRanger.
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