Read mapping formats
| File type | Suffix | Import | Export | Description |
|---|---|---|---|---|
| ACE | .ace | X | X | No chromatogram or quality score |
| AGP | .agp/.fa | X | Exports scaffolded contigs (see below) | |
| BAM | .bam | X | X | Compressed version of SAM. See SAM import |
| CLC | .clc | X | X | Rich format including all information |
| CLC Assembly File | .cas | X | Output from the CLC Assembly Cell | |
| SAM | .sam | X | X | Sequence Alignment/Map. See Sequence assembly files |
| Mapping coverage | .tsv | X | Detailed per-base info on coverage (see below) |
Note about BAM export Index files can be created as part of BAM exports.
Note about AGP format Both sequence lists and contigs with reads mapped can be used. Based on annotations of type Scaffold (which are automatically added when running the de novo assembly with the scaffold option), the contigs are broken up before exported as fasta. The agp file produced holds information about how the contigs relate to each other.
Export of coverage information from read mappings
Coverage information from read mappings can be exported in a tabular format using Mapping Coverage export. The output contains information on the number of nucleotides aligned to positions of reference sequences. Insertions are also reported, as described below while deletions are reported as reference regions without read coverage. Both stand-alone read mappings and reads tracks can be used as input.
The exported file contains the following columns:
| Column | Description |
| 1 | Reference name |
| 2 | Reference position |
| 3 | Reference sub-position (insertion) |
| 4 | Reference symbol |
| 5 | Number of As |
| 6 | Number of Cs |
| 7 | Number of Gs |
| 8 | Number of Ts |
| 9 | Number of Ns |
| 10 | Number of Gaps |
| 11 | Total number of reads covering the position |
The Reference sub-position column is empty (indicated by a - symbol) when the reference is defined at a given position. In case of an insertion this column contains an index into the insertion (a number between 1 and the length of the insertion) while the Reference symbol column is empty and the Reference position column contains the position of the last reference.
The "Export all columns" option is selected by default. When it is deselected, options for selecting the columns to export are presented in the next wizard step.
When selecting specific columns for export, the option "Export the table as currently shown" is particularly useful if you have filtered, sorted, or selected particular columns in a table that is open in a View. In this case, the effects of these manipulations are preserved in the exported file. This option is not available for all data types.
When the "Export the table as currently shown" is unchecked or disabled, checkboxes for each column to be exported are available to select or deselect. The buttons below that section can help speed up the process of column selection:
- All Select all possible columns.
- None Clear the existing selection.
- Default Select a standard set of columns, as defined by the software for this data type.
- Last export Select the columns that were selected during the most recent previous export.
- Active View Select the same set of columns as those selected in the Side Panel of the open data element. This button is only visible if the element being exported is in an open View.
In the final wizard step, select the location where the exported elements should be saved.