Torrent Browser Analysis Report Guide

Torrent Suite Software space on Ion Community

Output Files

These links permit you to directly download the data and report files.Some files are compressed, using the .zip format, to provide data integrity and to reduce download time.

Click on a file type button to save the file to your local computer.Most outputfiles can be loaded into third-party viewers (such as IGV) for visualization. The barcode row only appears for runs on barcoded data.

Files in the barcode row are zips of one file per active barcode. To download only BAM and BAI files for a single barcode, go to the barcode section at the top of the run report (see Barcode Reports ).

Column	Description
Reads	Files with unaligned reads (before alignment)
Aligned Reads	Files with aligned reads

File type

Reads

Aligned reads

BAM

Unaligned reads in BAM format.

In this release, the BAM file contains some flow space information.

Aligned reads sorted by reference location.

See Run Metrics Overview for a description of the alignment data included in this BAM file.

BAI

BAM index file

The BAM format

Binary Sequence Alignment/Map (BAM), is a compressed, binary form of the SAM format. BAM files can be indexed, using the BAM Index file, for quick access to sequence alignment data. See http://samtools.sourceforge.net for more a more detailed description of the SAM/BAM file format. Many tools are available for working with SAM files.

Deprecated file formats

The following file formats are deprecated and not produced by the default analysis pipeline. The FileExporter Plugin optionally generates these files.

Icon

The SFF and FASTQ files created by the FileExporter Plugin are generated in the plugin directory , not in the main analysis directory

.

File type

Description

SFF

Compressed (.zip) Standard Flowgram Format (SFF) -formatted file that contains "flow space" data.

The bases called in a run are stored in two formats: SFF and FASTQ. Both files contain the nucleotide calls and associated quality values, the SFF files, additionally, contain signal values in flow space and a mapping between sequence and flow spaces.

The data are organized on a per flow basis, and contain information about nucleotide flows that both did and did not result in base incorporation. (See Technical Note - Filtering and Trimming .)

Note: The SFF file format is deprecated and not produced by the default pipeline.

FASTQ

Compressed (.zip)FASTQ-formatted file containing data organized in a per-base basis, including quality scores. The reads contained in the file are unaligned reads. (See Technical Note - Filtering and Trimming .)

Note: The FASTQ file format is deprecated and not produced by the default pipeline.

Rename your output files

See the FileExporter Plugin supports renaming your putput files. (This plugin also optionally creates SFF or FASTQ formats, or zips your output.)

Contents

Torrent Browser Analysis Report Guide

Run Report Metrics

Run Metrics Overview

Run Report Metrics Before Alignment

Run Report Metrics on Aligned Reads

Compare Multiple Run Reports

Barcode Reports

Test Fragment Report

Report Information

Output Files

Plugin Summary

Run the Installed Plugins

Assembler SPAdes Plugin

Coverage Analysis Plugin

ERCC Analysis Plugin

FileExporter Plugin

FilterDuplicates Plugin

IonReporterUploader Plugin

See The Ion Reporter™ Software Integration Guide

Run RecognitION Plugin

SampleID Plugin

TorrentSuiteCloud Plugin

Torrent Variant Caller Plugin

Torrent Variant Caller Parameters

Example Torrent Variant Caller Parameter File

Torrent Variant Caller Output

The Command-Line Torrent Variant Caller

Ion Reporter™ Software Features Related to Variant Calling

Integration with TaqMan® and PCR

Classic Run Reports