STAR solo

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. It's used to generate count matrix for each sample. For this you need to provide :

• Fastq folder : It is necessary to adhere to the conventional naming convention when naming FASTQ files that are generated by the 10x Genomics platform while uploading fastq folder.
• Cell barcode whitelist : a list of known cell barcodes that are expected to be present in a particular biological sample
• Indexed genome folder using STAR : there is a task that permits to do that
• UMI start position , UMI length and cell barcode length.