"EFO:0010891" for scATAC-seq that is also a descendant of "EFO:0008913" for single-cell RNA sequencing
+
+unpaired assay: "EFO:0010891" for scATAC-seq or its descendants that is not a descendant of "EFO:0008913" for single-cell RNA sequencing
+
+## scATAC-seq asset Dataset Criteria
+
+A Dataset MUST meet each of the following criteria in order to be eligible for scATAC-seq assets:
+* the obs['assay_ontology_term_id'] values MUST all be paired assays or MUST all be unpaired assays
+* the obs['is_primary_data'] values MUST be all True
+* the var['feature_reference'] values MUST include one of "NCBITaxon:9606" for Homo sapiens or "NCBITaxon:10090" for Mus musculus, but not both. The value that is present will determine the appropriate Chromosome Table for standards.
+
+If the obs['assay_ontology_term_id'] values are all paired assays then the Dataset MAY have a fragments file asset.
+
+If the obs['assay_ontology_term_id'] values are all unpaired assays then the Dataset MUST have a fragments file asset.
+
+
+## scATAC-seq Asset: Fragments File (submitted)
+
+This MUST be a gzipped tab-separated values (TSV) file.
+
+The curator MUST annotate the following header-less columns. Additional columns and header lines beginning with `#` MUST NOT be included.
+
+### first column
+
+| Annotator | +Curator MUST annotate. | +
|---|---|
| Value | +str. This MUST be the reference genome chromosome the fragment is located on. The value MUST be one of the values from the Chromosome column in the appropriate Chromosome Table.
+ |
+
| Annotator | +Curator MUST annotate. | +
|---|---|
| Value | +int. This MUST be the 0-based start coordinate of the fragment.
+ |
+
| Annotator | +Curator MUST annotate. | +
|---|---|
| Value | +int. This MUST be the 0-based end coordinate of the fragment. The end position is exclusive, so represents the position immediately following the fragment interval. The value MUST be greater than the start coordinate specified in the second column and less than or equal to the Length of the Chromosome specified in the first column, as specified in the appropriate Chromosome Table.
+ |
+
| Annotator | +Curator MUST annotate. | +
|---|---|
| Value | +str. This MUST be the cell identifier. The value MUST be found in the obs index of the associated Dataset. Every obs index value of the associated Dataset MUST appear at least once in this column of the fragments file.
+ |
+
| Annotator | +Curator MUST annotate. | +
|---|---|
| Value | +int. This MUST be the total number of read pairs associated with this fragment. The value MUST be 1 or greater.
+ |
+
{dataset_version_id}-fragments.tsv.gz, a tab-separated values (TSV) file position-sorted and compressed by bgzip.
+
+## scATAC-seq Asset: Fragments File index
+
+From every fragments file (processed) asset, CELLxGENE Discover MUST generate {dataset_version_id}-fragments.tsv.gz.tbi, a tabix index of the fragment intervals from the fragments file.
+
+## Chromosome Tables
+
+As determined by the reference assembly used by the gene annotation versions pinned for this version of the schema. Only chromosomes or scaffolds that have at least one gene feature present are included.
+
+### human (GRCh38.p14)
+
+| Chromosome | +Length | +
|---|---|
| chr1 | +248956422 | +
| chr2 | +242193529 | +
| chr3 | +198295559 | +
| chr4 | +190214555 | +
| chr5 | +181538259 | +
| chr6 | +170805979 | +
| chr7 | +159345973 | +
| chr8 | +145138636 | +
| chr9 | +138394717 | +
| chr10 | +133797422 | +
| chr11 | +135086622 | +
| chr12 | +133275309 | +
| chr13 | +114364328 | +
| chr14 | +107043718 | +
| chr15 | +101991189 | +
| chr16 | +90338345 | +
| chr17 | +83257441 | +
| chr18 | +80373285 | +
| chr19 | +58617616 | +
| chr20 | +64444167 | +
| chr21 | +46709983 | +
| chr22 | +50818468 | +
| chrX | +156040895 | +
| chrY | +57227415 | +
| chrM | +16569 | +
| GL000009.2 | +201709 | +
| GL000194.1 | +191469 | +
| GL000195.1 | +182896 | +
| GL000205.2 | +185591 | +
| GL000213.1 | +164239 | +
| GL000216.2 | +176608 | +
| GL000218.1 | +161147 | +
| GL000219.1 | +179198 | +
| GL000220.1 | +161802 | +
| GL000225.1 | +211173 | +
| KI270442.1 | +392061 | +
| KI270711.1 | +42210 | +
| KI270713.1 | +40745 | +
| KI270721.1 | +100316 | +
| KI270726.1 | +43739 | +
| KI270727.1 | +448248 | +
| KI270728.1 | +1872759 | +
| KI270731.1 | +150754 | +
| KI270733.1 | +179772 | +
| KI270734.1 | +165050 | +
| KI270744.1 | +168472 | +
| KI270750.1 | +148850 | +
| Chromosome | +Length | +
|---|---|
| chr1 | +195154279 | +
| chr2 | +181755017 | +
| chr3 | +159745316 | +
| chr4 | +156860686 | +
| chr5 | +151758149 | +
| chr6 | +149588044 | +
| chr7 | +144995196 | +
| chr8 | +130127694 | +
| chr9 | +124359700 | +
| chr10 | +130530862 | +
| chr11 | +121973369 | +
| chr12 | +120092757 | +
| chr13 | +120883175 | +
| chr14 | +125139656 | +
| chr15 | +104073951 | +
| chr16 | +98008968 | +
| chr17 | +95294699 | +
| chr18 | +90720763 | +
| chr19 | +61420004 | +
| chrX | +169476592 | +
| chrY | +91455967 | +
| chrM | +16299 | +
| GL456210.1 | +169725 | +
| GL456211.1 | +241735 | +
| GL456212.1 | +153618 | +
| GL456219.1 | +175968 | +
| GL456221.1 | +206961 | +
| GL456239.1 | +40056 | +
| GL456354.1 | +195993 | +
| GL456372.1 | +28664 | +
| GL456381.1 | +25871 | +
| GL456385.1 | +35240 | +
| JH584295.1 | +1976 | +
| JH584296.1 | +199368 | +
| JH584297.1 | +205776 | +
| JH584298.1 | +184189 | +
| JH584299.1 | +953012 | +
| JH584303.1 | +158099 | +
| JH584304.1 | +114452 | +
| Key | +peak_grouping | +
|---|---|
| Annotation | +Curator MAY annotate if the Dataset has a fragments file asset; otherwise, this key MUST NOT be present. | +
| Value | +
+ str. The value MUST match a key in obs. If annotated, genome track assets MUST be submitted. The following columns MUST NOT be specified:
+
cell_type.+ |
+
uns['peak_grouping'] is annotated, there MUST be exactly one genome track asset submitted for each unique value in the obs column specified as determined by anndata.obs.{peak_grouping_column}.unique(). Otherwise, this MUST NOT be submitted.
+
+Asset file specifications TBD based on the visualization solution. Accepting .bigWig format is a requirement.