TReFID ~ Control C ~ Project Input File
 

The input data for a TReFID analysis are stored in a single file. This input file has the extension ".project" and contains TAB-delimited text as shown in the table below (get the file here; it is already included in TReFID package for download). The header section contains user-supplied information about the project. Each enzyme has its own header section with similar data fields; these fields are all empty in this case. The tRF data proper are listed below the header. The first two columns contain the dye code (1 = JOE) and peak numbers. The tRF size is a hundredfold the actual value; thus a value of 15382 means the fragment's extrapolated size was 154 nt.  The peak height and area values given in the last two columns are relative fluorscence values (rfu), as in the GeneScan software; in this project these values were not obtained experimentally but randomly created and are therefore meaningless.

 

Back to Figure 5

 

>Project Data:

Project title:
Project created on:
Sample:
Primers:
Notes:

In_Silico
Tuesday, 11.Nov.03 (10:53)
Database_Excerpt
63f-JOE
mixture of three strains (AbrSp7+EcoO157:H7+RleWSM1698)

 

>tRF Data:

>AluI:

Source:
Sample:
Date:
Primers:
Notes:

<Source>
<Sample>
<Date>
<Primers>
<Note>

 

Dye

Peak

Size

Height

Area

1

1

4000

785

1037

1

2

17100

388

48

1

3

22600

101

874

 

 

>Bme1390I:

Source:
Sample:
Date:
Primers:
Notes:

<Source>
<Sample>
<Date>
<Primers>
<Note>

 

Dye

Peak

Size

Height

Area

1

1

40200

987

233

1

2

41500

611

492

 

 

>Bsh1236I:

Source:
Sample:
Date:
Primers:
Notes:

<Source>
<Sample>
<Date>
<Primers>
<Note>

 

Dye

Peak

Size

Height

Area

1

1

6000

711

3372

1

2

17300

593

4163

1

3

36000

698

6881

 

 

>Cfr13I:

Source:
Sample:
Date:
Primers:
Notes:

<Source>
<Sample>
<Date>
<Primers>
<Note>

 

Dye

Peak

Size

Height

Area

1

1

16100

427

3175

1

2

16700

338

2595

1

3

25500

506

3917

 

 

>HaeIII:

Source:
Sample:
Date:
Primers:
Notes:

<Source>
<Sample>
<Date>
<Primers>
<Note>

 

Dye

Peak

Size

Height

Area

1

1

3600

139

674

1

2

17100

936

1618

1

3

19000

253

731

 

 

>Hin6I:

Source:
Sample:
Date:
Primers:
Notes:

<Source>
<Sample>
<Date>
<Primers>
<Note>

 

Dye

Peak

Size

Height

Area

1

1

4500

107

443

1

2

30200

810

5301

1

3

33600

742

3231

 

 

>HinfI:

Source:
Sample:
Date:
Primers:
Notes:

<Source>
<Sample>
<Date>
<Primers>
<Note>

 

Dye

Peak

Size

Height

Area

1

1

6600

179

1625

1

2

27400

166

437

1

3

29500

325

901

 

 

>MboI:

Source:
Sample:
Date:
Primers:
Notes:

<Source>
<Sample>
<Date>
<Primers>
<Note>

 

Dye

Peak

Size

Height

Area

1

1

20400

358

1927

1

2

21700

785

2709

1

3

23800

403

2937

 

 

>MspI:

Source:
Sample:
Date:
Primers:
Notes:

<Source>
<Sample>
<Date>
<Primers>
<Note>

 

Dye

Peak

Size

Height

Area

1

1

11500

842

3028

1

2

36600

612

5694

1

3

46100

974

7931

 

 

>RsaI:

Source:
Sample:
Date:
Primers:
Notes:

<Source>
<Sample>
<Date>
<Primers>
<Note>

 

Dye

Peak

Size

Height

Area

1

1

39200

799

7401

 

 

>TaiI:

Source:
Sample:
Date:
Primers:
Notes:

<Source>
<Sample>
<Date>
<Primers>
<Note>

 

Dye

Peak

Size

Height

Area

1

1

6500

853

5339

1

2

14300

782

3007

1

3

48100

193

1906

 

 

>TaqI:

Source:
Sample:
Date:
Primers:
Notes:

<Source>
<Sample>
<Date>
<Primers>
<Note>

 

Dye

Peak

Size

Height

Area

1

1

48900

234

2102

 

 

>TasI:

Source:
Sample:
Date:
Primers:
Notes:

<Source>
<Sample>
<Date>
<Primers>
<Note>

 

Dye

Peak

Size

Height

Area

1

1

45700

948

274

1

2

47000

876

5706

 

Back to Figure 5