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comparison SAINT_preprocessing.xml @ 26:f2102787b4ff draft

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author bornea
date Mon, 18 Apr 2016 10:23:31 -0400
parents 9a110e634afe
children 2d78642361c3
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25:9a110e634afe 26:f2102787b4ff
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 ^^^^^^^^^^^^^^^^^^^^^^^
85 84
86 APOSTL is able to recognize either a Scaffold *Samples Report* file 85 APOSTL is able to recognize either a Scaffold *Samples Report* file
87 (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
88 MaxQuant *txt* output folder. No modifications should be made to these 87 MaxQuant *txt* output folder. No modifications should be made to these
89 files. Please designate which one is being provided. 88 files. Please designate which one is being provided.
90 89
91 2) Scaffold or MaxQuant File Input 90 *2) Scaffold or MaxQuant File Input*
92 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
93 91
94 Select the corresponding *Samples Report* or *peptides.txt* here. 92 Select the corresponding *Samples Report* or *peptides.txt* here.
95 93
96 3) Create Prey File 94 *3) Create Prey File*
97 ^^^^^^^^^^^^^^^^^^^
98 95
99 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.
100 97
101 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
102 (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
105 SAINTexpress using the same data set while changing which baits are 102 SAINTexpress using the same data set while changing which baits are
106 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**
107 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
108 file can be used for both SAINTexpress runs. 105 file can be used for both SAINTexpress runs.
109 106
110 4) Provide Uniprot FASTA database 107 *4) Provide Uniprot FASTA database*
111 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
112 108
113 Please specify a FASTA file containing the protein sequence. You can 109 Please specify a FASTA file containing the protein sequence. You can
114 download the latest release of Uniprot's reviewed sequences (Swiss-Prot) 110 download the latest release of Uniprot's reviewed sequences (Swiss-Prot)
115 http://www.uniprot.org/downloads. For computing efficiency, 111 http://www.uniprot.org/downloads. For computing efficiency,
116 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
117 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
118 database searches during peptide and protein ID. 114 database searches during peptide and protein ID.
119 115
120 5) Are You Providing Your Own Bait File? 116 *5) Are You Providing Your Own Bait File?*
121 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
122 117
123 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
124 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
125 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
126 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.
127 122
128 6) Bait File 123 *6) Bait File*
129 ^^^^^^^^^^^^
130 124
131 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
132 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
133 to the **Bait Create** tool. 127 to the **Bait Create** tool.
134 128
135 **Note:** Individual bait names must match to the sample names 129 **Note:** Individual bait names must match to the sample names
136 within your Scaffold or MaxQuant output exactly and must contain no 130 within your Scaffold or MaxQuant output exactly and must contain no
137 whitespace characters (e.g. spaces) or dashes. 131 whitespace characters (e.g. spaces) or dashes.
138 132
139 7) Bait Create 133 *7) Bait Create*
140 ^^^^^^^^^^^^^^
141 134
142 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.
143 136
144 **Note:** Individual bait names must match to the sample names 137 **Note:** Individual bait names must match to the sample names
145 within your Scaffold or MaxQuant output exactly and must contain no 138 within your Scaffold or MaxQuant output exactly and must contain no