Table 1.
Expected outputs for single-cell read alignment and DropEst library quantification
| Object attribute (within .bam or .rds) | Definition | Step output |
|---|---|---|
| NH | Number of reported alignments that contain the query in the current record. | Step 3 .bam, Step 4 .bam |
| HI | Query hit index, indicating the alignment record is the i-th one stored in SAM. | Step 3 .bam, Step 4 .bam |
| AS | Alignment score generated by aligner | Step 3 .bam, Step 4 .bam |
| nM | Number of mismatches per (paired) alignment | Step 3 .bam, Step 4 .bam |
| GX | Gene id | Step 4 .bam |
| CR | Cell barcode raw | Step 4 .bam |
| UR | UMI raw | Step 4 .bam |
| CB | Cell barcode | Step 4 .bam |
| UB | UMI | Step 4 .bam |
| Cm | Count matrix in sparse format | Step 4 .rds |
| cm_raw | Count matrix in sparse format without filtration by minimal number of UMI and by the required type of reads (-L option) | Step 4 .rds |
| saturation_info | Data for estimating saturation using preseqR package | Step 4 .rds |
| merge_targets | Vector of corrected barcodes, named with raw barcodes | Step 4 .rds |
| aligned_reads_per_cell | Number of aligned reads per cell | Step 4 .rds |
| aligned_umis_per_cell | Number of aligned UMIs per cell | Step 4 .rds |
| requested_umis_per_cb | Number of UMIs per cell | Step 4 .rds |
| requested_reads_per_cb | Number of reads per cell | Step 4. rds |