Export Consensus Sequence

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Export Consensus Sequence

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Overview

In September 2017, we have implemented a new function in the Genome Browser to export consensus sequences from .bam alignment tracks. This will allow users to easily compare how their aligned sequences compare to the reference genome used for the alignment. This feature will also output the frequency with which reads from an alignment match the consensus sequence.

Workflow Actions

To run this module in the Genome Browser, users must narrow a genome location to less than 250 bp in length. First, choose the option to "Show Read Sequence" above the .bam file name:

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Then, simply right-click within the alignment track and choose the option to "Export Consensus Sequence for Selected Track" or "Export Consensus Sequence for All Tracks"

You will be prompted for a location to save the output files.


Input Data Requirements

This function requires .bam alignment files.

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Output Results

There will be two output files with the name specified (.fasta and .txt):


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The FASTA file will contain 1) the Reference sequence for these genomic coordinates 2) the Consensus sequence for each .bam file (or just the selected bam file)


Fasta output.png


The accompanying .txt file will contain tab-delimited information related to each consensus sequence derived, including: 1) Reference position of each nucleotide in the consensus sequence 2) Percentage of calls that match the consensus site 3) Coverage – TOTAL (consensus and all other nucleotides) number of reads mapping to the referenced position The name of the .bam file will be used to populate the Sample field:


Txt output.png

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