> For the complete documentation index, see [llms.txt](https://help.idm.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/custom/bed.md).

# Reference BED

A BED-like tab-separated value (TSV) file with no header row and with 4 or 5 columns:

1. `accession`: each sequence accession as it appears in Custom Reference FASTA header
2. `start`: start position (always set to 0)
3. `end`: end position (sequence length)
4. `genome`: full name of the virus the sequence belongs to (e.g. Influenza A H1N1)
5. (optional) `segment`: how this sequence is labeled within the virus (e.g. Segment 4 (HA)). Set to 'Full' if the sequence is the full genome

## Guidelines

* This file affects how sequences are labeled in the output.
* Sequence names must match those in Custom Reference FASTA. The same set of sequences must appear in both.
* If there are multiple viruses, their names should be unique. For example, if there are multiple Influenza genomes, they should not be labeled with the same virus name in the 4th column.
* If the Custom Reference FASTA includes sequences from multiple segments, it is strongly recommended to provide this BED file. Otherwise, each segment will be treated independently and not all of them may be used as reference.

## Example

```
NC_012532.1 0   10794   Zika    Full
NC_007373.1 0   2341    Influenza A virus (H3N2)    Segment 1 (PB2)
NC_007372.1 0   2341    Influenza A virus (H3N2)    Segment 2 (PB1)
NC_007371.1 0   2233    Influenza A virus (H3N2)    Segment 3 (PA+PA-X)
NC_007366.1 0   1762    Influenza A virus (H3N2)    Segment 4 (HA)
NC_007369.1 0   1566    Influenza A virus (H3N2)    Segment 5 (NP)
NC_007368.1 0   1467    Influenza A virus (H3N2)    Segment 6 (NB+NA)
NC_007367.1 0   1027    Influenza A virus (H3N2)    Segment 7 (M1+M2)
NC_007370.1 0   890     Influenza A virus (H3N2)    Segment 8 (NS1+NEP)
```


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/custom/bed.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.