Why are Torrents counted under “Hotspot” data? If Mobile Hotspot is included in the customers plan, Hotspot draws from the monthly data bucket Mobile Hotspot Allocation of the plan. This includes usage associated with: Allowing other users to connect to your device via Mobile Hotspot feature. Connect a device such as a laptop or tablet to the Internet either via Wi-Fi, or a physical connection such as a USB cable , or an app that enables mobile hotspot service without the purchase of a hotspot plan i.
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When applied to a reference genome in the Torrent Browser, these files perform these two functions: Targeted regions of interest Specifies your regions of interest, for instance the amplified regions that are used with targeted sequencing. The complete Torrent Suite Software a nalysis pipeline, including plugins, is restricted to only the specified regions. BED file only Hotspot Instructs the Variant Caller to include these positions in its output files, including evidence for a variant and the filtering thresholds that disqualified a variant candidate.
A hotspots file affects only the variantCaller plugin, not other parts of the a nalysis pipeline. In the template and planned run wizard, menus on the Reference chevron page offer the BED and VCF files that you uploaded to a reference. Notes about hotspot files: By default the variantCaller plugin calls variant candidates at hotspot positions with more sensitivity than candidates at other positions.
You can customize certain variantCaller parameters separately for hotspot candidates. Icon Target regions BED files provide an option to restrict the analysis of the entire reference genome.
Whole genome analysis is supported by the run type Whole Genome Analysis. Do not specify a t arget regions BED file on the Planning tab run registration page if the variants are to be called over the whole genome. Icon All regions specified in your t arget regions BED files are analyzed. Follow the instructions in Modify a BED File before uploading your Target regions BED file to delete lines representing regions that span variants that you do not wish to call. Icon The BED file coordinates example: The start position is included, and the range extends up to, but not including, the end position.
Icon BED files used with Ion AmpliSeq workflows define the internal segment only, and do not include the primer sequence. Torrent Suite Software reference genomes are sorted alpha-numerically not by a chromosome sort. If you upload your own reference genome, the BED and VCF files that you use with that reference must be sorted by the same method as your reference file. Summary of steps to add a target regions or hotspots file Before your analysis run or run registration on the Planning page , you can add BED or VCF files to your genome reference: Your new file also appears in the Target Regions or HotSpots menus in the template and planned run wizard References chevron.
You can use this technique to avoid regions for which you do not want variants called even if the variants appear in your sample.
Follow these instructions to modify a BED file: Make a copy of your BED file. Rename the two files in a way that reflects changes you make to the regions being analyzed. Open the BED file with a text editor. Delete the lines for regions you do not want. Save the file. Supported file types Targeted regions of interest BED file only. Supported file extensions are. These instructions apply to both targeted regions of interest files and hotspot regionsfiles.
You have the responsibility to avoid the following mismatch errors. The uploader does not always detect these errors: In the Reference tab, click either the Hotspots or Target Regions tab in the left navigation panel: The Hotspots or Target Regions page opens: Click the Select File button and browse to the file to be uploaded. In the Reference menu, be careful to select the correct reference. The new file can only be used with this reference.
Add the optional but recommended description and notes. Wait while the file is validated: For large files, verification can take a couple minutes.
Refresh your browser to check that validation is complete. After upload After validation, the Torrent Browser opens to the Hotspots detail page for your new file: From this page, you can download the hotspots file or target regions file, remove the file from the system, and view the validation log. Upload errors Validation errors appear in the Processing Log section of the details page. Some types of error do not appear in the Processing Log section.
There are major problems that prevent validation from being attempted: Incorrect file format Zip contains 0 or multiple files A corrupted. Go to the admin References tab and click either the Hotspots or Target Regions tab in the left navigation panel: In the Hotspots or Target Regions page, click the name: In the details page, click the link in the Processed File field: The Original File link in the Original Upload section also downloads the same file. Delete a hotspots or target regions file Icon This step removes the file from the system.
There is no recovery or undo. Consider first downloading the file as a backup. Follow these steps to delete a hotspots or a target regions file: In the details page, go to the Original Upload section and click the Delete button.
If you are sure, click Yes in the confirmation popup. BED file formats and examples.
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