From 2cb0215534369cc9d4776585857d981cd0bf5555 Mon Sep 17 00:00:00 2001 From: Kevin Ha Date: Wed, 16 Mar 2022 21:00:58 -0400 Subject: [PATCH] Update README --- README.md | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 4d86cd1..0bbefc1 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ other tools such as [Sailfish](https://github.com/kingsfordgroup/sailfish) and ## Installation -QAPA consists of both Python (3.5+) and R scripts. A conda virtual environment +QAPA consists of both Python and R scripts. A conda virtual environment can be created using the provided `environment.yml` file. 1. Clone the repo: @@ -32,6 +32,9 @@ can be created using the provided `environment.yml` file. mamba env create -f environment.yml conda activate qapa +4. Test that `qapa` command is available + + qapa --help --- # Usage @@ -170,6 +173,14 @@ Additional notes: - 3' UTRs that contain introns will be skipped. - Chromosome names that contain underscores are currently not supported and will be skipped. + - Only genes with `Gene Type = 'protein_coding'` will be considered. + +### Troubleshooting tips + + - Use `--debug` option to produce more verbose logging messages + - Use `--save` and `--temp ` to save intermediate files generated + by `qapa build`. `` should be a user accessible directory. + ## 2) Extract 3′ UTR sequences (`fasta`)