Mercurial > repos > bornea > saint_preprocessing
comparison SAINT_preprocessing.xml @ 24:85c19ee579d6 draft
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author | bornea |
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date | Mon, 18 Apr 2016 10:17:48 -0400 |
parents | 59b2553c6db5 |
children | 9a110e634afe |
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23:59b2553c6db5 | 24:85c19ee579d6 |
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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 |
79 This tool will read in a Scaffold *Samples Report* file (tab-delimited | 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 | 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. | 81 a *Bait File, Prey File,* and *Inter File* for SAINTexpress analysis. |
82 | 82 |
83 1) MaxQuant or Scaffold | 83 1) MaxQuant or Scaffold |
84 ----------------------- | 84 ^^^^^^^^^^^^^^^^^^^^^^^ |
85 | 85 |
86 APOSTL is able to recognize either a Scaffold *Samples Report* file | 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 | 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 | 88 MaxQuant *txt* output folder. No modifications should be made to these |
89 files. Please designate which one is being provided. | 89 files. Please designate which one is being provided. |
90 | 90 |
91 2) Scaffold or MaxQuant File Input | 91 2) Scaffold or MaxQuant File Input |
92 ---------------------------------- | 92 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
93 | 93 |
94 Select the corresponding *Samples Report* or *peptides.txt* here. | 94 Select the corresponding *Samples Report* or *peptides.txt* here. |
95 | 95 |
96 3) Create Prey File | 96 3) Create Prey File |
97 ------------------- | 97 ^^^^^^^^^^^^^^^^^^^ |
98 | 98 |
99 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. |
100 | 100 |
101 When making a prey file, APOSTL queries a user provided FASTA database | 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 | 102 (see below) in order to extract protein amino acid lengths and gene |
106 considered test or control. It is useful to toggle **Create Prey File** | 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 | 107 off in order to save time by circumventing this step as the same prey |
108 file can be used for both SAINTexpress runs. | 108 file can be used for both SAINTexpress runs. |
109 | 109 |
110 4) Provide Uniprot FASTA database | 110 4) Provide Uniprot FASTA database |
111 --------------------------------- | 111 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
112 | 112 |
113 Please specify a FASTA file containing the protein sequence. You can | 113 Please specify a FASTA file containing the protein sequence. You can |
114 download the latest release of Uniprot's reviewed sequences (Swiss-Prot) | 114 download the latest release of Uniprot's reviewed sequences (Swiss-Prot) |
115 at http://www.uniprot.org/downloads. For computing efficiency, | 115 http://www.uniprot.org/downloads. For computing efficiency, |
116 please limit your FASTA file to your species of interest. It is | 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 | 117 generally advised to use the same FASTA database that was used for your |
118 database searches during peptide and protein ID. | 118 database searches during peptide and protein ID. |
119 | 119 |
120 5) Are You Providing Your Own Bait File? | 120 5) Are You Providing Your Own Bait File? |
121 ---------------------------------------- | 121 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
122 | 122 |
123 Users have two options for providing a *Bait* file. If you would like to | 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 | 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 | 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. | 126 within Galaxy, please select No and proceed to the **Bait Create** tool. |
127 | 127 |
128 6) Bait File | 128 6) Bait File |
129 ------------ | 129 ^^^^^^^^^^^^ |
130 | 130 |
131 If you selected Yes above, please specify the *Bait* file you would like | 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 | 132 to provide. If you selected No above, ignore this argument and proceed |
133 to the **Bait Create** tool. | 133 to the **Bait Create** tool. |
134 | 134 |
135 **Note:** Individual bait names must match to the sample names | 135 **Note:** Individual bait names must match to the sample names |
136 within your Scaffold or MaxQuant output exactly and must contain no | 136 within your Scaffold or MaxQuant output exactly and must contain no |
137 whitespace characters (e.g. spaces) or dashes. | 137 whitespace characters (e.g. spaces) or dashes. |
138 | 138 |
139 7) Bait Create | 139 7) Bait Create |
140 -------------- | 140 ^^^^^^^^^^^^^^ |
141 | 141 |
142 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. |
143 | 143 |
144 **Note:** Individual bait names must match to the sample names | 144 **Note:** Individual bait names must match to the sample names |
145 within your Scaffold or MaxQuant output exactly and must contain no | 145 within your Scaffold or MaxQuant output exactly and must contain no |