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comparison SAINT_preprocessing.xml @ 24:85c19ee579d6 draft

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author bornea
date Mon, 18 Apr 2016 10:17:48 -0400
parents 59b2553c6db5
children 9a110e634afe
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23:59b2553c6db5 24:85c19ee579d6
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