Joined August 2012
- Tweets 148
- Following 125
- Followers 772
- Likes 18
6 Photos and videos
5 May 2021
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
6
98
291
5 May 2021
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
1
1
7
5 May 2021
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
1
4
11
29 Dec 2020
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…
1
3
21
16 Jun 2020
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.
53
162
28 Apr 2020
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
1
5
28 Apr 2020
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
Alex Dobin retweeted
31 Mar 2020
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/…
3
23
57
Alex Dobin retweeted
12 Dec 2019
A few word on our recent manuscript, “The transcriptional legacy of developmental stochasticity”
biorxiv.org/content/10.1101/…
(0/18)
5
24
43
Alex Dobin retweeted
12 Dec 2019
The transcriptional legacy of developmental stochasticity biorxiv.org/content/10.1101/…
5
8
14 Nov 2019
STARsolo poster from #gi2019 is available on f1000 Genome Informatics Conference Collection:
doi.org/10.7490/f1000researc…
11
22
Alex Dobin retweeted
13 Nov 2019
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…
4
8
Alex Dobin retweeted
21 Oct 2019
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.…
16
30
8 Oct 2019
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
2
43
113
14 Aug 2019
STAR 2.7.2a:
github.com/alexdobin/STAR/re…
Major improvements in chimeric detection and reporting, contributed by Brian Haas @brianjhaas.
18
53
15 May 2019
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.
4
55
118
Alex Dobin retweeted
6 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
5 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.
1
34
49
24 Jan 2019
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.
2
77
149