<commit_before>STAR 2.7.0a 2019/01/23
======================

STARsolo: mapping, demultiplexing and gene quantification for single cell RNA-seq
---------------------------------------------------------------------------------
STARsolo is a turnkey solution for analyzing droplet single cell RNA sequencing data (e.g. 10X Genomics Chromium System) built directly into STAR code.
STARsolo inputs the raw FASTQ reads files, and performs the following operations 
* error correction and demultiplexing of cell barcodes using user-input whitelist
* mapping the reads to the reference genome using the standard STAR spliced read alignment algorithm
* error correction and collapsing (deduplication) of Unique Molecular Identifiers (UMIa) 
* quantification of per-cell gene expression by counting the number of reads per gene

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.

The STAR solo algorithm is turned on with:
```
--soloType Droplet 
```

Presently, the cell barcode whitelist has to be provided with:
``` 
--soloCBwhitelist /path/to/cell/barcode/whitelist
```

The 10X Chromium whitelist file can be found inside the CellRanger distribution, 
e.g. [10X-whitelist](https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-whitelist-).
Please make sure that the whitelist is compatible with the specific version of the 10X chemistry (V1,V2,V3 etc).

Importantly, in the --readFilesIn option, the 1st file has to be cDNA read, and the 2nd file has to be the barcode (cell+UMI) read, i.e.<commit_msg>Minor changes to changes and release notes.<commit_after>STAR 2.7.0a 2019/01/23
======================

STARsolo: mapping, demultiplexing and gene quantification for single cell RNA-seq
---------------------------------------------------------------------------------
STARsolo is a turnkey solution for analyzing droplet single cell RNA sequencing data (e.g. 10X Genomics Chromium System) built directly into STAR code.
STARsolo inputs the raw FASTQ reads files, and performs the following operations 
* error correction and demultiplexing of cell barcodes using user-input whitelist
* mapping the reads to the reference genome using the standard STAR spliced read alignment algorithm
* error correction and collapsing (deduplication) of Unique Molecular Identifiers (UMIa) 
* quantification of per-cell gene expression by counting the number of reads per gene

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.

The STAR solo algorithm is turned on with:
```
--soloType Droplet 
```

Presently, the cell barcode whitelist has to be provided with:
``` 
--soloCBwhitelist /path/to/cell/barcode/whitelist
```

The 10X Chromium whitelist file can be found inside the CellRanger distribution, 
e.g. [10X-whitelist](https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-whitelist-).
Please make sure that the whitelist is compatible with the specific version of the 10X chemistry (V1,V2,V3 etc).

Importantly, in the --readFilesIn option, the 1st file has to be cDNA read, and the 2nd file has to be the barcode (cell+UMI) read, i.e.
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