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comparison SAINT_preprocessing.xml @ 27:2d78642361c3 draft

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author bornea
date Mon, 18 Apr 2016 10:25:06 -0400
parents f2102787b4ff
children 8031a47f67c6
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26:f2102787b4ff 27:2d78642361c3
78 txt file) or a MaxQuant *peptides.txt* file and process them to generate 78 txt file) or a MaxQuant *peptides.txt* file and process them to generate
79 a *Bait File, Prey File,* and *Inter File* for SAINTexpress analysis. 79 a *Bait File, Prey File,* and *Inter File* for SAINTexpress analysis.
80 80
81 -------------- 81 --------------
82 82
83 *1) MaxQuant or Scaffold* 83 **1) MaxQuant or Scaffold**
84 84
85 APOSTL is able to recognize either a Scaffold *Samples Report* file 85 APOSTL is able to recognize either a Scaffold *Samples Report* file
86 (tab-delimited txt file) or the *peptides.txt* file output in the 86 (tab-delimited txt file) or the *peptides.txt* file output in the
87 MaxQuant *txt* output folder. No modifications should be made to these 87 MaxQuant *txt* output folder. No modifications should be made to these
88 files. Please designate which one is being provided. 88 files. Please designate which one is being provided.
89 89
90 *2) Scaffold or MaxQuant File Input* 90 **2) Scaffold or MaxQuant File Input**
91 91
92 Select the corresponding *Samples Report* or *peptides.txt* here. 92 Select the corresponding *Samples Report* or *peptides.txt* here.
93 93
94 *3) Create Prey File* 94 **3) Create Prey File**
95 95
96 Select whether or not you would like APOSTL to generate a prey file. 96 Select whether or not you would like APOSTL to generate a prey file.
97 97
98 When making a prey file, APOSTL queries a user provided FASTA database 98 When making a prey file, APOSTL queries a user provided FASTA database
99 (see below) in order to extract protein amino acid lengths and gene 99 (see below) in order to extract protein amino acid lengths and gene
102 SAINTexpress using the same data set while changing which baits are 102 SAINTexpress using the same data set while changing which baits are
103 considered test or control. It is useful to toggle **Create Prey File** 103 considered test or control. It is useful to toggle **Create Prey File**
104 off in order to save time by circumventing this step as the same prey 104 off in order to save time by circumventing this step as the same prey
105 file can be used for both SAINTexpress runs. 105 file can be used for both SAINTexpress runs.
106 106
107 *4) Provide Uniprot FASTA database* 107 **4) Provide Uniprot FASTA database**
108 108
109 Please specify a FASTA file containing the protein sequence. You can 109 Please specify a FASTA file containing the protein sequence. You can
110 download the latest release of Uniprot's reviewed sequences (Swiss-Prot) 110 download the latest release of Uniprot's reviewed sequences (Swiss-Prot)
111 http://www.uniprot.org/downloads. For computing efficiency, 111 http://www.uniprot.org/downloads. For computing efficiency,
112 please limit your FASTA file to your species of interest. It is 112 please limit your FASTA file to your species of interest. It is
113 generally advised to use the same FASTA database that was used for your 113 generally advised to use the same FASTA database that was used for your
114 database searches during peptide and protein ID. 114 database searches during peptide and protein ID.
115 115
116 *5) Are You Providing Your Own Bait File?* 116 **5) Are You Providing Your Own Bait File?**
117 117
118 Users have two options for providing a *Bait* file. If you would like to 118 Users have two options for providing a *Bait* file. If you would like to
119 create your own *Bait* file, select Yes and designate the file below. If 119 create your own *Bait* file, select Yes and designate the file below. If
120 you would like to use the **Bait Create** tool to create a *Bait* file 120 you would like to use the **Bait Create** tool to create a *Bait* file
121 within Galaxy, please select No and proceed to the **Bait Create** tool. 121 within Galaxy, please select No and proceed to the **Bait Create** tool.
122 122
123 *6) Bait File* 123 **6) Bait File**
124 124
125 If you selected Yes above, please specify the *Bait* file you would like 125 If you selected Yes above, please specify the *Bait* file you would like
126 to provide. If you selected No above, ignore this argument and proceed 126 to provide. If you selected No above, ignore this argument and proceed
127 to the **Bait Create** tool. 127 to the **Bait Create** tool.
128 128
129 **Note:** Individual bait names must match to the sample names 129 **Note:** Individual bait names must match to the sample names
130 within your Scaffold or MaxQuant output exactly and must contain no 130 within your Scaffold or MaxQuant output exactly and must contain no
131 whitespace characters (e.g. spaces) or dashes. 131 whitespace characters (e.g. spaces) or dashes.
132 132
133 *7) Bait Create* 133 **7) Bait Create**
134 134
135 Using the **Bait Create** tool, you can create your *bait.txt* file. 135 Using the **Bait Create** tool, you can create your *bait.txt* file.
136 136
137 **Note:** Individual bait names must match to the sample names 137 **Note:** Individual bait names must match to the sample names
138 within your Scaffold or MaxQuant output exactly and must contain no 138 within your Scaffold or MaxQuant output exactly and must contain no