DataFormat

Location

Applies to:  Sequence and Sequence Collection

Description

The "Location" format is used to describe the location of sequences. The format lists one sequence on each line in the output with multiple TAB-separated columns containing different information. Several varieties of the format exists with different number of fields, either 10, 8 or 4. In addition, there is a 6-field format that can only be used for input (read by MotifLab). If the predefined formats are not enough, it is also possible to define new custom formats.

10-field format
  1. Sequence identifier
  2. Organism (taxonomy ID)
  3. Genome build
  4. Chromosome
  5. Start of sequence segment (genomic coordinate)
  6. End of sequence segment (genomic coordinate)
  7. Gene name (this could be the same as the sequence ID)
  8. Transcription start site for the gene (genomic coordinate). This is optional and can be set to NULL
  9. Transcription end site for the gene (genomic coordinate). This is optional and can be set to NULL
  10. The strand orientation of the sequence/gene. (DIRECT, +1, +) or (REVERSE, -1, -)

Examples
ENSG00000111249  9606  hg18  12  109954212  109956411  CUX2    109956212  110272739  Direct
ENSG00000187664  9606  hg18  19   19244979   19247178  HAPLN4   19245178   19226557  Reverse
ENSG00000196358  9606  hg18   9  134025155  134027354  NTNG2   134027155  134109742  -


8-field format

The 8-field format is a subset of the columns in the 10-field format with the organism identifier and gene name omitted.
The organism is then derived from the genome build and the gene name is set to the same as the sequence identifier.
  1. Sequence identifier
  2. Genome build
  3. Chromosome
  4. Start of sequence segment (genomic coordinate)
  5. End of sequence segment (genomic coordinate)
  6. Transcription start site for the gene (genomic coordinate). This is optional and can be set to NULL
  7. Transcription end site for the gene (genomic coordinate). This is optional and can be set to NULL
  8. The strand orientation of the sequence/gene. (DIRECT, +1, +) or (REVERSE, -1, -)

Examples
UNG      hg18    12    108017798    108019997    108019798    NULL       DIRECT BRCA2    hg18    13     31785617     31787816     31787617    NULL       + HAPLN4   hg18    19     19244979     19247178     19245178    19226557   Reverse


6-field format

This format specifies the locations of sequences relative known genes. Note that this format can only be used as input.
  1. Gene identifier (depending on type)
  2. Name of gene identifier type (e.g. "Ensembl Gene", "Entrez Gene" or "HGNC Symbol")
  3. Genome build
  4. Start of sequence segment relative to anchor point (see field #6)
  5. End of sequence segment relative to anchor point (see field #6)
  6. Anchor point. This could either be "TSS", "TES". MotifLab v2 also supports the anchor "full gene".

Examples
NTNG1             HGNC Symbol    hg18    -2000    200    TSS 56475             Entrez Gene    hg18    -2000    200    TSS ENSG00000111249   Ensembl Gene   hg18    -2000    200    TSS ENSG00000187664   Ensembl Gene   hg18    -2000    200    TSS ENSG00000196358   Ensembl Gene   hg18    -2000    200    TSS


4-field format
  1. Sequence identifier
  2. Chromosome
  3. Start of sequence segment (genomic coordinate)
  4. End of sequence segment (genomic coordinate)
There is also a "relative 4-field format" which is similar to the regular 4-field format with one exception. If a sequence is associated with the reverse strand, the start and end coordinates will be swapped so that the value in the 3rd column is larger than the value in the 4th column.


Custom format

When the "custom format" is used, the fields to output and how to separate them can be specified manually by describing a string containing special field codes. The following field codes are recognized (case-insensitive):
Example: the custom format "Sequence name,chromosome,start,end" will be similar to the standard 4-field format except that commas are used instead of TABs to separate to fields (to insert TABs use the escape code: \t )

Arguments

NameDescription
Format The version of the format to use for output. Valid options are:
  • 10 field format
  • 8 field format
  • 4 field format
  • 4 field format (relative)
  • Custom format
These formats are described above
Custom Format If "Custom Format" is selected for the "Format" parameter, the format string must be specified with this parameter as described above for the custom format.
add CHR prefix If this option is selected, a "chr" prefix will be added to the chromosome number when outputting chromosomes.
Strand notation This parameter specifies what notation to use to output the strand orientation of sequences. Valid options are "Direct/Reverse", "+1/-1" or "+/-".

See Also: output