diff SAINT_preprocessing.xml @ 23:59b2553c6db5 draft

Uploaded

--- a/SAINT_preprocessing.xml	Sat Apr 16 16:36:48 2016 -0400
+++ b/SAINT_preprocessing.xml	Mon Apr 18 10:07:50 2016 -0400
@@ -81,7 +81,7 @@
 a *Bait File, Prey File,* and *Inter File* for SAINTexpress analysis.
 
 1) MaxQuant or Scaffold
-^^^^^^^^^^^^^^^^^^^^^^^
+-----------------------
 
 APOSTL is able to recognize either a Scaffold *Samples Report* file
 (tab-delimited txt file) or the *peptides.txt* file output in the
@@ -89,12 +89,12 @@
 files. Please designate which one is being provided.
 
 2) Scaffold or MaxQuant File Input
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+----------------------------------
 
 Select the corresponding *Samples Report* or *peptides.txt* here.
 
 3) Create Prey File
-^^^^^^^^^^^^^^^^^^^
+-------------------
 
 Select whether or not you would like APOSTL to generate a prey file.
 
@@ -108,7 +108,7 @@
 file can be used for both SAINTexpress runs.
 
 4) Provide Uniprot FASTA database
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+---------------------------------
 
 Please specify a FASTA file containing the protein sequence. You can
 download the latest release of Uniprot's reviewed sequences (Swiss-Prot)
@@ -118,7 +118,7 @@
 database searches during peptide and protein ID.
 
 5) Are You Providing Your Own Bait File?
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+----------------------------------------
 
 Users have two options for providing a *Bait* file. If you would like to
 create your own *Bait* file, select Yes and designate the file below. If
@@ -126,7 +126,7 @@
 within Galaxy, please select No and proceed to the **Bait Create** tool.
 
 6) Bait File
-^^^^^^^^^^^^
+------------
 
 If you selected Yes above, please specify the *Bait* file you would like
 to provide. If you selected No above, ignore this argument and proceed
@@ -137,7 +137,7 @@
     whitespace characters (e.g. spaces) or dashes.
 
 7) Bait Create
-^^^^^^^^^^^^^^
+--------------
 
 Using the **Bait Create** tool, you can create your *bait.txt* file.