updating scripts directory README

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.