Merge branch 'make_metadata' of github.com:Arcadia-Science/2022-mtx-n…

…ot-in-mgx-pairs into make_metadata

README.md

@@ -1,7 +1,7 @@
 # Identifying sequences that are in a metatranscriptome but not in a metagenome
 
 This repository curates a set of paired metagenomes and metatranscriptomes and provides a pipeline to rapidly identify the fraction of sequences in a metatranscriptome that are not in a metagenome.
-The pipeline is shaped around a metadata file, 'inputs/metadata-paired-mgx-mtx.tsv', that contains a sample name (`sample_name`), metagenome SRA run accession (`mgx_run_accession`; `SRR*`, `ERR*`, `DRR*`), metatranscriptome SRA run accession (`mtxx_run_accession`), and a sample type (`sample_type`).
+The pipeline is shaped around a metadata file, 'inputs/metadata-paired-mgx-mtx.tsv', that contains a sample name (`sample_name`), metagenome SRA run accession (`mgx_run_accession`; `SRR*`, `ERR*`, `DRR*`), metatranscriptome SRA run accession (`mtx_run_accession`), and a sample type (`sample_type`).
 Using the run accessions, it downloads the sequencing data from the SRA and generates a [FracMinHash sketch](https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2.abstract) of each run.
 Then, it uses the paired information encoded in the metadata table to subtract the metagenome sketch from the metatranscriptome sketch.
 This produces an estimate of the fraction metatranscriptome sequences not found in the paired metagenome.