From af1276a2c5739a05dd2fc041c8528d64fbf91c6a Mon Sep 17 00:00:00 2001 From: Nathan Roach Date: Sun, 19 Jan 2020 16:10:37 -0500 Subject: [PATCH] updating scripts directory README --- scripts/README.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/scripts/README.md b/scripts/README.md index b7be1b8..38ba6b6 100644 --- a/scripts/README.md +++ b/scripts/README.md @@ -1,9 +1,8 @@ -#Scripts directory README +# Scripts directory README.md -Directions for replicating the analysis in "The full length transcriptome of C. elegans". -*At the moment the file paths in these scripts are explicit paths to files on my machine. This will change as I update the files for better & easier reproducibility. Until then you may have to change the file paths to reflect the directory structure of your machine.* +For replicating the analysis you'll mostly want to be interacting with master\_script.bsh in the directory above this one. -If you plan to replicate the poly(A) profiling estimation, start in the data directory and run download\_fast5.bsh to download the necessary data and set up the directory structure required. Then start in this directory by running the scripts in 00\_basecalling\_and\_adapter\_trimming/ and making your way through the directories in the numbered order they appear. +For understanding what is being done in that master script you're in the right place. -If you plan to only replicate the clustering and UTR estimation, start in the data directory and run download\_fastq.bsh to download the necessary data and set up the directory structures required. Then start in this directory by running the scripts in 01\_alignment/ and making your way through the directories in the numbered order they appear. +Master script and the scripts it calls visit these directories mostly in the numbered order of the subdirectories of this folder, with the exception of 09\_polyacalling/, which was added slightly later.