Sequence Properties

Description

The Sequence_Properties format will output a table with one sequence on each row and with columns containing information about different sequence properties chosen by the user.

Example of properties output with the format string "name, gene name, organism name, chromosome, genomic start, genomic end" (with header)

#name gene name organism name chromosome genomic start genomic end ENSG00000035403 VCL Human 10 75425878 75428077 ENSG00000100345 MYH9 Human 22 35113759 35115958 ENSG00000107796 ACTA2 Human 10 90702310 90704509 ENSG00000130176 CNN1 Human 19 11508579 11510778 ENSMUSG00000017167 Cntnap1 Mouse 11 101168523 101170722

Arguments

Name	Description
Format	This parameter specifies which sequence properties to include in the output as an ordered, comma-separated list of property names. Note that standard properties are case-insensitive, but user-defined properties are case-sensitive! Standard sequence properties include: name gene name chromosome genomic start genomic end TSS[0]-relative start TSS[0]-relative end TES[0]-relative start TES[0]-relative end TSS[1]-relative start TSS[1]-relative end TES[1]-relative start TES[1]-relative end TSS TES length organism ID organism name organism latin name genome build orientation orientation string orientation sign The genomic coordinates returned by genomic start, genomic end, TSS and TES assumes that the chromosome starts at position 1, but it is possible to return zero-based coordinates by adding the suffix "[0]" directly behind these properties. E.g. the property "genomic start[0]" will return a number which is one less than the regular "genomic start". The "TSS/TES[n]-relative" coordinates returns the start or end of the sequence relative to the position of TSS or TES. If the number within the brackets is 0, the position of TSS/TES will be 0 with downstream bases having increasing positive coordinates and upstream bases having increasing negative coordinates. If the number in the brackets is [1], the position of TSS/TES is +1, the immediate downstream base is at +2 and the immediate upstream base is at -1 (hence, the counting skips 0 and goes directly from -1 to +1 at TSS/TES).
Separator	This parameter specifies how to separate the sequence properties on each line in the output. The character chosen as the separator will replace the commas in the format string above. Valid options for the separator are "TAB" (default), "Comma", "Semicolon", "Colon" and "Vertical bar".
List-separator	Some sequence properties may be represented by lists (e.g. GO-terms). The "List-separator" parameter specifies how to separate the entries in such lists. Valid options are "Comma" (default), "TAB", "Semicolon", "Colon" and "Vertical bar". Note that this separator should be different from the separator used to separate the sequence properties that are output.
Header	If this option is selected, a header line starting with # will be included at the beginning of the output. The header line describes which sequence properties are included.

Name

Description

Format

This parameter specifies which sequence properties to include in the output as an ordered, comma-separated list of property names. Note that standard properties are case-insensitive, but user-defined properties are case-sensitive!

Standard sequence properties include:

name
gene name
chromosome
genomic start
genomic end
TSS[0]-relative start
TSS[0]-relative end
TES[0]-relative start
TES[0]-relative end
TSS[1]-relative start
TSS[1]-relative end
TES[1]-relative start
TES[1]-relative end
TSS
TES
length
organism ID
organism name
organism latin name
genome build
orientation
orientation string
orientation sign

The genomic coordinates returned by genomic start, genomic end, TSS and TES assumes that the chromosome starts at position 1, but it is possible to return zero-based coordinates by adding the suffix "[0]" directly behind these properties. E.g. the property "genomic start[0]" will return a number which is one less than the regular "genomic start". The "TSS/TES[n]-relative" coordinates returns the start or end of the sequence relative to the position of TSS or TES. If the number within the brackets is 0, the position of TSS/TES will be 0 with downstream bases having increasing positive coordinates and upstream bases having increasing negative coordinates. If the number in the brackets is [1], the position of TSS/TES is +1, the immediate downstream base is at +2 and the immediate upstream base is at -1 (hence, the counting skips 0 and goes directly from -1 to +1 at TSS/TES).

Separator

This parameter specifies how to separate the sequence properties on each line in the output. The character chosen as the separator will replace the commas in the format string above. Valid options for the separator are "TAB" (default), "Comma", "Semicolon", "Colon" and "Vertical bar".

List-separator

Some sequence properties may be represented by lists (e.g. GO-terms). The "List-separator" parameter specifies how to separate the entries in such lists. Valid options are "Comma" (default), "TAB", "Semicolon", "Colon" and "Vertical bar". Note that this separator should be different from the separator used to separate the sequence properties that are output.

Header

If this option is selected, a header line starting with # will be included at the beginning of the output. The header line describes which sequence properties are included.

output

Motif_Properties

Module_Properties

Properties