Download BAM files

You must have an Ion Reporter™ Software account on an Ion Reporter™ Server to complete this procedure. You cannot download BAM files from Ion Reporter™ Software on Thermo Fisher™ Connect Platform.

IMPORTANT! If you have data from BAM files that you intend to store long term, you can archive the data. For more information, see Archive analyses to an external storage device.

You can download a BAM file that is generated by Ion Reporter™ Software to review the file, or open the file and inspect the data with a visualization tool outside of the software. The BAM index file (BAI) is included in the download.

The software gives you the option to download the BAM files, if one or more BAM files are available for an analysis. The following BAM files are available in Ion Reporter™ Software for completed analyses:

  • If only RNA samples are analyzed, a mapped BAM is available in for download.

  • For DNA samples, two BAM files can be available for download: a mapped BAM and a processed BAM.

A mapped BAM is a file that maps the BAM file that is uploaded to Ion Reporter™ Software to the reference genome and based on selected alignment parameters. The processed BAM file, that is available only for DNA samples, is the BAM file that contains the reads processed by Variant Caller module in Ion Reporter™ Software, where read trimming and read filtering can be applied.

Note: The processed BAM file is much smaller than the mapped BAM file. For DNA samples, download the processed BAM to a computer for review to save time and computer hard drive disk space.

  1. In the Analyses tab, click Overview, then select the analysis of interest.
  2. Select one of the following options:

    • Click Actions > Download Processed BAM to download the BAM file that was processed by the Variant Caller in Ion Reporter™ Software.

    • Select Actions > Download Mapped BAM download the BAM file that is mapped to the reference genome, based on selected alignment parameters.

  3. To download the BAM file from Ion Reporter™ Software:
    1. Click the Home tab, then click Notifications.
    2. Find the download file in the list. You can click Downloads to narrow the list or see the timestamp.
    3. Click (Download).

    A file that used the naming convention analysisName_bamFileType_bam.zip is downloaded. The file contains the BAM files and the associated BAI file. The mapped BAM file is named merged.bam and the processed BAM is named merged.bam.ptrim.bam. An unmapped BAM file is named the same as the file name that was used to define the samples used in the analysis launch.

Related Topics
Parent topic: Analyses