Mercurial > repos > bornea > saint_preprocessing
comparison SAINT_preprocessing.xml @ 21:d9592cc1df99 draft
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author | bornea |
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date | Sat, 16 Apr 2016 16:28:07 -0400 |
parents | 0ac97a6298c2 |
children | d3bb9de6913b |
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20:0ac97a6298c2 | 21:d9592cc1df99 |
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69 <param name="input" value="fa_gc_content_input.fa"/> | 69 <param name="input" value="fa_gc_content_input.fa"/> |
70 <output name="out_file1" file="fa_gc_content_output.txt"/> | 70 <output name="out_file1" file="fa_gc_content_output.txt"/> |
71 </test> | 71 </test> |
72 </tests> | 72 </tests> |
73 <help> | 73 <help> |
74 # Pre-Processing | 74 Pre-Processing |
75 ============== | |
75 | 76 |
76 * * * | 77 -------------- |
77 | 78 |
78 This tool will read in a Scaffold _Samples Report_ file (tab-delimited txt file) or a MaxQuant _peptides.txt_ file and process them to generate a _Bait File, Prey File,_ and _Inter File_ for SAINTexpress analysis. | 79 This tool will read in a Scaffold *Samples Report* file (tab-delimited |
80 txt file) or a MaxQuant *peptides.txt* file and process them to generate | |
81 a *Bait File, Prey File,* and *Inter File* for SAINTexpress analysis. | |
79 | 82 |
80 #### 1) MaxQuant or Scaffold | 83 1) MaxQuant or Scaffold |
84 ^^^^^^^^^^^^^^^^^^^^^^^ | |
81 | 85 |
82 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. | 86 APOSTL is able to recognize either a Scaffold *Samples Report* file |
87 (tab-delimited txt file) or the *peptides.txt* file output in the | |
88 MaxQuant *txt* output folder. No modifications should be made to these | |
89 files. Please designate which one is being provided. | |
83 | 90 |
84 #### 2) Scaffold or MaxQuant File Input | 91 2) Scaffold or MaxQuant File Input |
92 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
85 | 93 |
86 Select the corresponding _Samples Report_ or _peptides.txt_ here. | 94 Select the corresponding *Samples Report* or *peptides.txt* here. |
87 | 95 |
88 #### 3) Create Prey File | 96 3) Create Prey File |
97 ^^^^^^^^^^^^^^^^^^^ | |
89 | 98 |
90 Select whether or not you would like APOSTL to generate a prey file. | 99 Select whether or not you would like APOSTL to generate a prey file. |
91 | 100 |
92 When making a prey file, APOSTL queries a user provided FASTA database (see below) in order to extract protein amino acid lengths and gene names. This may take several minutes depending on your computer and if your Galaxy distribution is cluster enabled. Some users may want to run SAINTexpress using the same data set while changing which baits are considered test or control. It is useful to toggle **Create Prey File** off in order to save time by circumventing this step as the same prey file can be used for both SAINTexpress runs. | 101 When making a prey file, APOSTL queries a user provided FASTA database |
102 (see below) in order to extract protein amino acid lengths and gene | |
103 names. This may take several minutes depending on your computer and if | |
104 your Galaxy distribution is cluster enabled. Some users may want to run | |
105 SAINTexpress using the same data set while changing which baits are | |
106 considered test or control. It is useful to toggle **Create Prey File** | |
107 off in order to save time by circumventing this step as the same prey | |
108 file can be used for both SAINTexpress runs. | |
93 | 109 |
94 #### 4) Provide Uniprot FASTA database | 110 4) Provide Uniprot FASTA database |
111 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
95 | 112 |
96 Please specify a FASTA file containing the protein sequence. You can download the latest release of Uniprot's reviewed sequences (Swiss-Prot) [here](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. | 113 Please specify a FASTA file containing the protein sequence. You can |
114 download the latest release of Uniprot's reviewed sequences (Swiss-Prot) | |
115 `here <http://www.uniprot.org/downloads>`__. For computing efficiency, | |
116 please limit your FASTA file to your species of interest. It is | |
117 generally advised to use the same FASTA database that was used for your | |
118 database searches during peptide and protein ID. | |
97 | 119 |
98 #### 5) Are You Providing Your Own Bait File? | 120 5) Are You Providing Your Own Bait File? |
121 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
99 | 122 |
100 Users have two options for providing a _Bait_ file. If you would like to create your own _Bait_ file, select <kbd>Yes</kbd> and designate the file below. If you would like to use the **Bait Create** tool to create a _Bait_ file within Galaxy, please select <kbd>No</kbd> and proceed to the **Bait Create** tool. | 123 Users have two options for providing a *Bait* file. If you would like to |
124 create your own *Bait* file, select Yes and designate the file below. If | |
125 you would like to use the **Bait Create** tool to create a *Bait* file | |
126 within Galaxy, please select No and proceed to the **Bait Create** tool. | |
101 | 127 |
102 #### 6) Bait File | 128 6) Bait File |
129 ^^^^^^^^^^^^ | |
103 | 130 |
104 If you selected <kbd>Yes</kbd> above, please specify the _Bait_ file you would like to provide. If you selected <kbd>No</kbd> above, ignore this argument and proceed to the **Bait Create** tool. | 131 If you selected Yes above, please specify the *Bait* file you would like |
132 to provide. If you selected No above, ignore this argument and proceed | |
133 to the **Bait Create** tool. | |
105 | 134 |
106 > **Note:** Individual bait names must match to the sample names within your Scaffold or MaxQuant output exactly and must contain no whitespace characters (e.g. spaces) or dashes. | 135 **Note:** Individual bait names must match to the sample names |
136 within your Scaffold or MaxQuant output exactly and must contain no | |
137 whitespace characters (e.g. spaces) or dashes. | |
107 | 138 |
108 #### 7) Bait Create | 139 7) Bait Create |
140 ^^^^^^^^^^^^^^ | |
109 | 141 |
110 Using the **Bait Create** tool, you can create your _bait.txt_ file. | 142 Using the **Bait Create** tool, you can create your *bait.txt* file. |
111 | 143 |
112 > **Note:** Individual bait names must match to the sample names within your Scaffold or MaxQuant output exactly and must contain no whitespace characters (e.g. spaces) or dashes. | 144 **Note:** Individual bait names must match to the sample names |
145 within your Scaffold or MaxQuant output exactly and must contain no | |
146 whitespace characters (e.g. spaces) or dashes. | |
113 | 147 |
114 APOSTL uses this bait file to find the user's baits of interest within a _Samples Report_ or _peptides.txt_ file and when preparing the _inter.txt_ file. | 148 APOSTL uses this bait file to find the user's baits of interest within a |
149 *Samples Report* or *peptides.txt* file and when preparing the | |
150 *inter.txt* file. | |
115 | 151 |
116 * * * | 152 -------------- |
117 | 153 |
118 Once your parameters have been finalized, please press the <kbd>Execute</kbd> button to start processing. This may take a few minutes. Once your process has been completed, you will see your _Bait File, Prey File,_ and _Inter File_ on the right hand side of your panel highlighted in green. | 154 Once your parameters have been finalized, please press the Execute |
155 button to start processing. This may take a few minutes. Once your | |
156 process has been completed, you will see your *Bait File, Prey File,* | |
157 and *Inter File* on the right hand side of your panel highlighted in | |
158 green. | |
119 </help> | 159 </help> |
120 </tool> | 160 </tool> |