dropEst - Pipeline¶
Pipeline for estimating molecular count matrices for droplet-based single-cell RNA-seq measurements.
General processing steps¶
- dropTag: extraction of cell barcodes and UMIs from the library. Result: demultiplexed .fastq.gz files, which should be aligned to the reference.
- Alignment of the demultiplexed files to reference genome. Result: .bam files with the alignment.
- dropEst: building count matrix and estimation of some statistics, necessary for quality control. Result: .rds file with the count matrix and statistics. Optionally: count matrix in MatrixMarket format.
- dropReport - Generating report on library quality.
- dropEstR - R pacakge for UMI count corrections and cell quality classification
Complete examples of the pipeline can be found at EXAMPLES.md.
- inDrop (v1-3)
If you find this pipeline useful for your research, please consider citing the paper:
Petukhov, V., Guo, J., Baryawno, N., Severe, N., Scadden, D. T., Samsonova, M. G., & Kharchenko, P. V. (2018). dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments. Genome biology, 19(1), 78. doi:10.1186/s13059-018-1449-6
- dropEstR package
- For developers