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Data availability

No sequencing reads, alignments, genome references, indexes, or large genomic tables are redistributed in this repository.

Public accessions

The Mature versus Memory comparison used:

  • Mature NK: SRR7650764, SRR7650846, SRR7650883, SRR7650911
  • Memory NK: SRR7650766, SRR7650808, SRR7650848, SRR7650885, SRR7650913, SRR7650922

The separate Week 1 training sample was SRR7650763 (Immature NK).

These accessions are associated with Calderon et al. (2019), https://doi.org/10.1038/s41588-019-0505-9. Retrieve public data from the appropriate NCBI archive and verify current archive metadata before reuse.

Inputs not included

Reproduction requires independently obtained and validated inputs:

  • paired FASTQ files for the Week 1 teaching exercise;
  • the ten comparison BAM/BAI pairs and sample-level broadPeak files, or a documented method to regenerate equivalent inputs;
  • GRCh38 reference resources;
  • an hg38 blacklist with compatible chromosome naming;
  • GENCODE Release 50 GRCh38 primary-assembly GTF and FASTA resources;
  • locally installed analysis software listed in environment/software_versions.tsv.

Local filesystem paths from the internship environment were deliberately removed. config/input_manifest.example.tsv shows the intended public format.