treeshop.md - fixed documentation for #22

treeshop.md

@@ -156,12 +156,13 @@ After this you should have the following under downstream:
               ├── methods.json
               └── mini.ann.vcf
 
-And the bam files generated by `expression` and `qc`  will be placed in `primary/derived` :
+The bam file generated by `qc`  will be placed in `primary/derived`. 
+Note that the bam file generated by `expression` (`sorted.bam`) is not downloaded at all.
 
 	treeshop/primary/derived
 	└── TEST
-	  ├── sorted.bam
-      └── sortedByCoord.md.bam
+	  ├── sortedByCoord.md.bam
+      └── sortedByCoord.md.bam.bai
 
 ### Shut Down