Metadata for Sections
About metadata for sections
Purpose of metadata for sections
Define and name sections of a reference sequence.
For references with many sections, it is more convenient, reproducible,
and traceable to define the sections in a file than on the command line,
using the option --sections-file (-s).
The sections file additionally permits giving each section a name.
Fields of metadata for sections
Name |
Type |
Description |
Required |
|---|---|---|---|
Section |
str |
Name of the section being defined |
yes |
Reference |
str |
Name of the reference of which the section is part |
yes |
5’ End |
int |
Coordinate of the section’s 5’ end (1-indexed, inclusive) |
no |
3’ End |
int |
Coordinate of the section’s 3’ end (1-indexed, inclusive) |
no |
Forward Primer |
str |
Sequence of the forward primer for the section |
no |
Reverse Primer |
str |
Sequence of the reverse primer for the section |
no |
Notes about metadata for sections
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 section. 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 section’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 section. 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 section’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 sections
Metadata for sections as a pretty table
Section |
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 sections as plain text
Section,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.