From 33fcfb918688eb5bb6013cdc60050c45148e0615 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Wed, 20 Mar 2024 11:29:29 +0000 Subject: [PATCH] update download reads and run commands --- README.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 6220c6e..047c0dd 100644 --- a/README.md +++ b/README.md @@ -54,15 +54,19 @@ To run on paired or unpaired Ion Torrent reads, use either of the above commands, but with the option `--tech iontorrent`. -You can run on a batch of reads, using a file -`runs.txt` of INSDC run accessions. -This will download each run from the ENA and run Viridian on it: +Download reads with accession SRR12345678 and run: ``` -viridian dl_and_run --acc_file runs.txt --outdir OUT +viridian run_one_sample --run_accession SRR12345678 --outdir OUT ``` The sequencing tech and unpaired/paired is taken from the ENA metadata for each run. +Download and run on a batch of sequencing runs, using a file +`runs.txt` of INSDC run accessions: +``` +viridian dl_and_run --acc_file runs.txt --outdir OUT +``` + ## Output files