CGHweb: File format help

File Types

CGHweb
Agilent
NimbleGen TXT
NimbleGen GFF

CGHweb File Type

The array-CGH data must be in text format and tab-delimited with the word "NA" to indicate missing log-ratios:

ProbeID	Chromosome	Position	LogRatio
Probe_1	1	100000	0.0735
Probe_2	1	110000	0.1520
Probe_3	1	120000	-0.1132

There should be following columns in the text file: ProbeID, Chromosome, Position, and LogRatio. The first line of the text file should contain these column names.
The values in the ProbeID column need to be unique. If ProbeId's are duplicate they will be marked duplicate_1,duplicate_2 by the program.
The data should be sorted by chromosome, then by position. The program will check if the data were sorted by position by chromosome and sort the data if they were unsorted.
The maximum upload file size is 30 megabytes. This should allow users to upload data from high-resolution array platforms (e.g., NimbleGen 385k, Agilent 244k). If your table is too large but has fewer than 500,000 probes, consider trimming the contents of the ProbeID column. We suggest uploading a very small file to test out the website before uploading a larger one for the actual analysis.
Please click here to see a sample file.

Agilent 244K Array

The files are tab delimited text files with one sample per file (called here a FE-file). Each FE-file has a total of 10 header lines broken into triplets of type, name, value lines for several variables and the first two blocks are delimited by a line with a ‘*’ character in column 1. The first triplet contains the type, name, and values for the Feature Extraction Parameters. The second triplet contains the type, name and values for a number of statistical or quality measures for that slide. After the ‘*’ break line the next two lines give the type and name of the raw data lines which are then followed by approx 240,000 lines of data for the various probes.

Columns used by CGHweb are:

Probe UID
SystematicName (chrN:startposition-endposition)
LogRatio

NimbleGen GFF File Format (general feature format file)

Columns with red font are used by the system

This is tab sperated file with following columns
1. Sequence name
2. Source
3. Feature
4. Start
5. End
6. Score
7. Strand
8. Frame
9. [attributes] [comments]
There are no header and comment lines in the file.
Probe IDs for these files are generated internally.
More information about GFF format can be found here.

NimbleGen TXT File Format

Columns with red font are used by the system

NimbleGen ".txt" files are tab sperated file. Where first line is the header to each column. The columns are
1. INDEX CONTAINER
2. SEQ_ID
3. PROBE_ID
4. POSITION
5. GC
6. CHROMOSOME
7. CHR_POSITION
8. EXP_?
9. REF_?
10. RATIO
11. EXP_NORM
12. REF_NORM
13. RATIO_CORRECTED
To see a sample file click here.