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Commit message:
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modified:
SAINT_preprocessing.xml |
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| diff -r f2102787b4ff -r 2d78642361c3 SAINT_preprocessing.xml --- a/SAINT_preprocessing.xml Mon Apr 18 10:23:31 2016 -0400 +++ b/SAINT_preprocessing.xml Mon Apr 18 10:25:06 2016 -0400 |
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| @@ -80,18 +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. @@ -104,7 +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) @@ -113,14 +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 @@ -130,7 +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. |