In certain workflows, you may be able to specify a Manifest file in the Reference Sequence screen.
Manifest files are tab-separated files used to define the chromosomal coordinates of gene targets in the assembly, and are normally generated automatically , e.g., by Illumina. (See Illumina’s manifest file PDF for a description.) Manifest files can have various file extensions, though .txt is commonly used.
SeqMan NGen can read and produce output using a variety of common chromosome naming conventions, including “chr1” and “ch1,” as well as Arabic and Roman numerals. Chromosome names are captured from genome template packages and used to assign contig IDs to entries from BED, VCF and manifest files.
The following examples show the most basic required columns for the manifest file, as well as two formats that are used by Illumina. These examples are provided in case you need to trouble-shoot problems with existing manifest files. If you want to create your own targeted regions file, we recommend making a BED file rather than a manifest file. See Make a custom BED file for detailed instructions.
The columns below can appear in any order. Columns with blue headers are required, while columns with orange headers are optional.
User-made file (most basic version):
| [Regions] | |||
|---|---|---|---|
| Name | Chromosome | Start | End |
| 28324371 | chrM | 577 | 647 |
Illumina manifest file – format 1:
| [Targets] | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| TargetA | TargetB | Target Number | Chromosome | Start Position | End Position | Probe Strand | Sequence | Species | Build ID |
| chr1.43815008.43815009 | chr1.43815008.43815009 | 1 | chr1 | 43814982 | 43815163 | + | GGTGCC | Homo sapiens | hg19 |
| chr1.115256528.115256531 | chr1.115256528.115256531 | 1 | chr1 | 115256500 | 115256680 | + | TCTTTA | Homo sapiens | hg19 |
Illumina manifest file – format 2:
| [Regions] | |||||
|---|---|---|---|---|---|
| Name | Chromosome | Start | End | Upstream Probe Length | Downstream Probe Length |
| 28324371 | chrM | 577 | 647 | 0 | 0 |
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