meeting-notes.markdown

@@ -65,3 +65,16 @@ End Goals:
 2016-12-13
 ============
 * Organize files by organism -> cell_type -> tf/hm -> (biorep1, biorep2, idr)
+
+2017-01-13
+===========
+* Modify ExpressOrtho perl script to confirm to perl style standards.
+* Fetch bams or fastqs.
+* Specify file accession for control and experiment instead of experiment accession.
+* Add IDR for 2 replicates.  Wait on response to figure out.  (IDR / FDR?)
+* MongoDB read only database to clone.  MongoDB helper scripts to update database.  Need to create own db instance for saving results.
+* Don't need to save output files back to the database.
+* Generate report log at the end.
+* Remove Duplicates yes / no & duplicates.
+* Pooled & Pseudo replicates - pooled concatenate, pseudo shuffled (bam -> sam for plaintext).  Configurable option.
+* Sphinx documentation at the same time.