Mercurial > repos > bornea > saint_preprocessing
changeset 24:85c19ee579d6 draft
Uploaded
| author | bornea |
|---|---|
| date | Mon, 18 Apr 2016 10:17:48 -0400 |
| parents | 59b2553c6db5 |
| children | 9a110e634afe |
| files | SAINT_preprocessing.xml |
| diffstat | 1 files changed, 9 insertions(+), 9 deletions(-) [+] |
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--- a/SAINT_preprocessing.xml Mon Apr 18 10:07:50 2016 -0400 +++ b/SAINT_preprocessing.xml Mon Apr 18 10:17:48 2016 -0400 @@ -72,7 +72,7 @@ </tests> <help> Pre-Processing -============== +-------------- -------------- @@ -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. @@ -108,17 +108,17 @@ 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) -at http://www.uniprot.org/downloads. For computing efficiency, +http://www.uniprot.org/downloads. For computing efficiency, please limit your FASTA file to your species of interest. It is generally advised to use the same FASTA database that was used for your 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.