Space Ranger2.0, printed on 12/26/2024
The spaceranger aggr pipeline outputs summary.json that contains metrics relating to the aggregated datasets. Note: Square brackets denote a variable that depends on the pipeline input,
such as, [library_id]_frac_reads_kept means that if your aggregation contains two libraries with IDs sample123 and sample456, there are two output metrics sample123_frac_reads_kept and sample456_frac_reads_kept.
| Metric | Description |
|---|---|
filtered_bcs_transcriptome_union | The estimated number of barcodes associated with a spot under tissue, summed across all input libraries. |
[pre/post]_total_reads | Total number of sequenced reads, summed across all input libraries. |
[pre/post]_multi_transcriptome_total_raw_reads_per_filtered_bc | total_reads divided by filtered_bcs_transcriptome_union. |
[library_id]_pre_normalization_raw_reads_per_filtered_bc | The mean total reads per spot prior to depth normalization, for the library denoted by library_id. |
[library_id]_pre_normalization_cmb_reads_per_filtered_bc | The mean confidently mapped and barcoded (CMB) reads per spot prior to depth normalization, for the library denoted by library_id. |
[library_id]_frac_reads_kept | The fraction of reads that were retained after depth normalization for the library denoted by library_id. |
lowest_frac_reads_kept | The lowest fraction of reads retained, corresponding to the library which lost the most reads during normalization. A low value may indicate a large disparity in the initial depth of the input libraries. |
If one or more of the aggregated samples was a Targeted Gene Expression sample, these additional metrics will also appear:
| Metric | Description |
|---|---|
[library_id]_pre_normalization_targeted_reads_per_filtered_bc | The mean targeted reads per spot prior to depth normalization, for the library denoted by library_id. |
[library_id]_frac_targeted_reads_kept | The fraction of reads mapped uniquely and confidently to targeted genes that were retained after depth normalization for the library denoted by library_id. This field will be shown instead of the metric [library_id]_frac_reads_kept above. |