2.7.0a STARsolo

[Alexander Dobin]

Dear All,

2.7.0a release introduces STARsolo, a turnkey solution for analyzing droplet single-cell RNA sequencing data (e.g. 10X Genomics Chromium System) built directly into STAR code.

The STARsolo output is designed to be a drop-in replacement for 10X CellRanger gene quantification output.

It follows CellRanger logic for cell barcode whitelisting and UMI deduplication and produces nearly identical gene counts in the same format.

At the same time, STARsolo is ~10 times faster than the CellRanger.

See the release notes and the manual for more information.

At the moment, STARsolo is designed with 10X Genomics Chromium protocol in mind, but I am working to incorporate other scRNA-seq protocols as well.

If you want a specific protocol incorporated, please send me a request with details on cDNA, cell barcode and UMI sequences.  

As always, questions/issues/feature requests are very welcome!

Also, I will start announcing STAR related news on my Twitter account @a_dobin

Cheers

Alex

[John S]

Hi Alex, just a quick question - STARsolo mode of STAR works only with Solo parameters? I.e. I shouldn't even be trying to use any other parameters that I would otherwise be using with standard STAR alignment?

[Alexander Dobin]

Hi John,

you can use other STAR parameters in the usual way in addition to the solo* parameters.

Of course, you need to be aware that the second - barcode - read is not processed in the normal way the paired-end reads are processed, so, for instance, you cannot clip it with STAR clip options.

I have not checked all possible combinations, so if you encounter any problems, please let me know.

Cheers

Alex

[Alexander Dobin]

Dear All,

2.7.0b is an important bug fix release replacing 2.7.0a.

Please note that you will need to re-generate genome index with the 2.7.0x releases.

Cheers

Alex

[Alexander Dobin]

Dear All,

yet another bugfix release for STARsolo: 2.7.0c

Cheers

Alex

[Alexander Dobin]

Dear All,

and another bugfix release for STARsolo: 2.7.0d

Cheers

Alex

[Alexander Dobin]

Dear All,

and yet another bugfix patch 2.7.0e

Cheers

Alex

[Dan]

Hello,

it would be great to have a real life example (or more?) for STARsolo.

Best regards,

Dan

[Matthew Thornton]

Hello!  I was wondering if there was a way to control the output from STARsolo similar to geneCounts in STAR. It would be desirable to get the count data for each cell as a massive spreadsheet.  Thank you for providing this important software.  I noticed that CellRanger uses STAR for alignment anyway so this is kind of a useful time saver.

[Alexander Dobin]

Hi Matthew,

STARsolo does output the per cell per gene read counts in the form of the sparse matrix in Solo.out/matrix.mtx - the same format as the Cell Ranger's.

Or do you have something else in mind?

Cheers

Alex