Galaxy |

RNA STARSolo (version 2.7.11a+galaxy1)

Custom or built-in reference genome:

Built-ins were indexed using default options

Reference genome with annotation:

Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions, and provide your own splice junction annonations.

Select reference genome:

If your genome of interest is not listed, contact the Galaxy team

Gene model (gff3,gtf) file for splice junctions:

Exon junction information for mapping splices

Elements to use from the gene model to use for splice junctions:

By default and for almost all cases: 'exon', referring to finding junctions at the RNA splice sites. This can optionally be changed to allow splicing at other levels, such as 'gene', 'transcript', 'CDS'.

Length of the genomic sequence around annotated junctions:

Used in constructing the splice junctions database. Ideal value is ReadLength-1

Type of single-cell RNA-seq:

Input Type:

RNA-Seq FASTQ/FASTA file, Barcode reads:

RNA-Seq FASTQ/FASTA file, cDNA reads:

RNA-Seq Cell Barcode Whitelist:

Configure Chemistry Options:

Barcode Size is same size of the Read:

Disable this if your R1 barcodes contain poly-T bases after the barcode sequence.

UMI deduplication (collapsing) algorithm:

All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, Exact collapses only exactly matching UMIs.

Matching the Cell Barcodes to the WhiteList:

Exact: only exact matches allowed; 1MM: only one match in whitelist with 1 mismatched base allowed. Allowed CBs have to have at least one read with exact match; 1MM_multi: multiple matches in whitelist with 1 mismatched base allowed, posterior probability calculation is used choose one of the matches; 1MM_multi_pseudocounts: same as 1MM_Multi, but pseudocounts of 1 are added to all whitelist barcodes.

Advanced Settings

Advanced Settings 0

Compute coverage:

outWigStrand:

What it does

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 takes raw FASTQ reads files as input, 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 (UMIs)

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 CellRanger.