Mercurial > repos > bornea > saint_preprocessing
changeset 26:f2102787b4ff draft
Uploaded
| author | bornea |
|---|---|
| date | Mon, 18 Apr 2016 10:23:31 -0400 |
| parents | 9a110e634afe |
| children | 2d78642361c3 |
| files | SAINT_preprocessing.xml |
| diffstat | 1 files changed, 7 insertions(+), 14 deletions(-) [+] |
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--- a/SAINT_preprocessing.xml Mon Apr 18 10:21:10 2016 -0400 +++ b/SAINT_preprocessing.xml Mon Apr 18 10:23:31 2016 -0400 @@ -80,21 +80,18 @@ -------------- -1) MaxQuant or Scaffold -^^^^^^^^^^^^^^^^^^^^^^^ +*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 MaxQuant *txt* output folder. No modifications should be made to these files. Please designate which one is being provided. -2) Scaffold or MaxQuant File Input -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +*2) Scaffold or MaxQuant File Input* Select the corresponding *Samples Report* or *peptides.txt* here. -3) Create Prey File -^^^^^^^^^^^^^^^^^^^ +*3) Create Prey File* Select whether or not you would like APOSTL to generate a prey file. @@ -107,8 +104,7 @@ off in order to save time by circumventing this step as the same prey file can be used for both SAINTexpress runs. -4) Provide Uniprot FASTA database -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +*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) @@ -117,16 +113,14 @@ 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? -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +*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 you would like to use the **Bait Create** tool to create a *Bait* file within Galaxy, please select No and proceed to the **Bait Create** tool. -6) Bait File -^^^^^^^^^^^^ +*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 @@ -136,8 +130,7 @@ within your Scaffold or MaxQuant output exactly and must contain no whitespace characters (e.g. spaces) or dashes. -7) Bait Create -^^^^^^^^^^^^^^ +*7) Bait Create* Using the **Bait Create** tool, you can create your *bait.txt* file.