Torrent Browser User Interface Guide
Torrent Suite Software space on Ion Community
Find the TMAP Command for a Completed Run
This page describes how to find the specific TMAP command and parameters that were used in a completed analysis.
-
In the run report for the analysis, click the
Plugin Summary
navigation button:
-
Click the
Support
tab.
-
Click the
View the report log
link.
- In the log file, search for tmap (lower case).
The following is an example TMAP command in the log file. In the log, the command appears as one long line and often is wrapped at the end of the line.
Aligning to reference genome in /results/referenceLibrary/tmap-f3/hg19
tmap mapall -n 24 -f /results/referenceLibrary/tmap-f3/hg19/hg19.fasta \
-r basecaller_results/recalibration/rawlib.basecaller.bam -v -Y -u \
--prefix-exclude 5 -o 2 stage1 map4 2>> \
basecaller_results/recalibration/rawlib/alignmentQC_out.txt > \
basecaller_results/recalibration/rawlib/samplelib.bam
Torrent Browser User Interface Guide
The Login Page
The Plan Tab
Templates
Planned Runs
Plan by Sample Set
Create Samples and a Sample Set
Sample Attributes
Template and Planned Run Wizard
Create Multiple Run Plans
Create a Template with Ion AmpliSeq.com Import
The Monitor Tab
The Data Tab
Completed Runs and Reports Tab
Work with Completed Runs
Reanalyze a Completed Run
BaseCaller Parameters
TMAP Parameters
The Projects Listing Page
Project Result Sets Page
Compare Multiple Run Reports
CSV Metrics File Format