Add 'rnaseq/step5_count/snippet_counts'

.drone.yml

@@ -7,6 +7,18 @@ steps:
 - name: lintr
   image: jupyter/datascience-notebook
   commands:
+  - export TAR="/bin/tar"
   - Rscript -e 'devtools::install_github("jimhester/lintr")'
-                  - Rscript -e 'lintr::lint_package()'
+  # Lint the document, printing output.
-
+  - |
+    Rscript -e 'lintr::lint_dir(
+      path=".", pattern=rex::rex(".", one_of("Rr"), maybe("md"), end)
+    )'
+  # Return non-zero exit code (no output is printed).
+  - |
+    Rscript -e 'quit(
+      save="no",
+      status=length(
+        lintr::lint_dir(path=".", pattern=rex::rex(".", one_of("Rr"), maybe("md"), end))
+      )
+    )'

rnaseq/README.md

@@ -0,0 +1,3 @@
+# RNAseq pipeline
+Snippets for the RNAseq pipeline:
+https://docs.google.com/document/d/1lM1wlz950Q8H6Oi7CWW28FO2tGv5nXYtW0wp8vEUizA

rnaseq/step5_count/snippet_counts

@@ -0,0 +1,18 @@
+## Generate Raw Counts using FeatureCounts/HTSeqCounts 
+
+## Load package Subread (packge within which FeatureCounts is present)
+
++ ml Subread/1.6.4-foss-2015b FeatureCounts
+
+## Features used in FeatureCounts : 
+## -s : reversely stranded 
+## -T : number of threads used 
+## -a : reference genome 
+## -o : output file 
+
++ featureCounts \
++ --a "path to reference genome" \
++ --T 6 \
++ --o "path to output file" \
++ --s 2
+