The procedure uses information from the core genes of six model organisms by first using TBLASTN to identify candidate regions in a new genome. It then proposes and redefines gene structures using a iterative combination of GeneWise, HMMER and geneid. The system includes the use of a profile for each core gene to ensure the reliability of the final predicted gene structure. CEGMA source code, compiled binaries and documentation are available under the GNU GENERAL PUBLIC LICENSE. Homepage: URL: ĭescription: Cell Ranger is a set of analysis pipelines that process Chromium single cell 3-RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3i-v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries.
Cell Ranger includes four main gene expression pipelines: - cellranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files.
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