Metadata for Regions
About metadata for regions
Purpose of metadata for regions
Define and name regions of a reference sequence.
For references with many regions, it is more convenient, reproducible,
and traceable to define the regions in a file than on the command line,
using the option --regions-file (-i).
The regions file additionally permits giving each region a name.
Fields of metadata for regions
Name |
Type |
Description |
Required |
|---|---|---|---|
Region |
str |
Name of the region being defined |
yes |
Reference |
str |
Name of the reference of which the region is part |
yes |
5’ End |
int |
Coordinate of the region’s 5’ end (1-indexed, inclusive) |
no |
3’ End |
int |
Coordinate of the region’s 3’ end (1-indexed, inclusive) |
no |
Forward Primer |
str |
Sequence of the forward primer for the region |
no |
Reverse Primer |
str |
Sequence of the reverse primer for the region |
no |
Notes about metadata for regions
Fields are case-sensitive and must be in the file’s first line.
The 5’ end can be defined in the field
5' End, which is a numeric coordinate, 1-indexed and included in the region. An alternative way to specify the 5’ end for amplicon-based samples is to type the forward primer in the fieldForward Primer. The primer must match the reference sequence exactly at exactly one location. The region’s 5’ end is placed downstream of the forward primer, with a gap whose length is set via the option--primer-gap.The 3’ end can be defined in the field
3' End, which is a numeric coordinate, 1-indexed and included in the region. An alternative way to specify the 3’ end for amplicon-based samples is to type the reverse primer in the fieldReverse Primer. The reverse complement of the primer must match the reference sequence exactly at exactly one location. The region’s 3’ end is placed upstream of the reverse primer, with a gap whose length is set via the option--primer-gap.
Example metadata for regions
Metadata for regions as a pretty table
Region |
Reference |
5’ End |
3’ End |
Forward Primer |
Reverse Primer |
|---|---|---|---|---|---|
5utr |
MyFavRNA |
1 |
103 |
||
cds |
MyFavRNA |
104 |
2368 |
||
3utr |
MyFavRNA |
2369 |
2695 |
||
thing1 |
OtherRef |
ACCCGTAACTATCG |
TACAGGTCCGCATG |
Metadata for regions as plain text
Region,Reference,5' End,3' End,Forward Primer,Reverse Primer
5utr,MyFavRNA,1,103,,
cds,MyFavRNA,104,2368,,
3utr,MyFavRNA,2369,2695,,
thing1,OtherRef,,,ACCCGTAACTATCG,TACAGGTCCGCATG
This text can be copied into a new CSV file.