mikessh commited on
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SOURCES: cite the scientific origin, not the internal staging path

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The data is TCGA/GDC -- public and citable on its own. The upstream staging
root said nothing the per-file relative paths below do not already carry.

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  1. SOURCES.md +2 -4
SOURCES.md CHANGED
@@ -7,15 +7,13 @@ re-formatted from experimental data.
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  | Artifact | Origin | Format | Provenance |
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  |---|---|---|---|
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- | `samples.tar.gz` | TCGA tumour bulk RNA-seq → AIRR clonotypes (internal *staging* pipeline) | tar.gz of per-sample AIRR TSVs | **experimental** (RNA-derived receptor rearrangements) |
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  | `metadata.tsv` | join of the source tables below, restricted to the 9,591 AIRR samples | TSV, keyed by `sample_id` | **derived** |
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  | `total_reads` (col) | GDC `rna_seq.genomic.gdc_realn.bam` `Total_Reads` | integer | **experimental** (raw library read total, all reads) |
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  | `aligned_reads` (col) | GDC realigned-BAM `Aligned_Reads` | integer | **experimental** (genome-aligned subset) |
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  | `metadata.hla.tsv` | HLA class-I: TCGA PanImmune (primary) ∪ OptiType-2017 fill, one row per donor | TSV, keyed by `subject_id`, `hla_source` col | **derived** (from experimental OptiType-based calls) |
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- ## Upstream sources (internal `staging`, 2025)
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-
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- Local root: `(internal staging)`
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  | Source | Path | Role |
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  |---|---|---|
 
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  | Artifact | Origin | Format | Provenance |
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  |---|---|---|---|
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+ | `samples.tar.gz` | TCGA tumour bulk RNA-seq → AIRR clonotypes (RNA-seq receptor profiling, Bolotin 2017) | tar.gz of per-sample AIRR TSVs | **experimental** (RNA-derived receptor rearrangements) |
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  | `metadata.tsv` | join of the source tables below, restricted to the 9,591 AIRR samples | TSV, keyed by `sample_id` | **derived** |
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  | `total_reads` (col) | GDC `rna_seq.genomic.gdc_realn.bam` `Total_Reads` | integer | **experimental** (raw library read total, all reads) |
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  | `aligned_reads` (col) | GDC realigned-BAM `Aligned_Reads` | integer | **experimental** (genome-aligned subset) |
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  | `metadata.hla.tsv` | HLA class-I: TCGA PanImmune (primary) ∪ OptiType-2017 fill, one row per donor | TSV, keyed by `subject_id`, `hla_source` col | **derived** (from experimental OptiType-based calls) |
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+ ## Upstream sources (internal staging, 2025)
 
 
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  | Source | Path | Role |
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  |---|---|---|