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Old 09-11-2018, 06:32 AM   #1
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Location: Netherlands

Join Date: Sep 2018
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Default Using Ion Reporter for data from other platforms

I have been using Ion Reporter (together with our Ion PGM and S5) for several years now and am really happy with this software.

Now I received data from an Illumina platform and was hoping to analyse this with the same software.

Has anybody else tried this before? And did you succeed?

The fastq files I got were aligned with bwa mem. The uploading of the bam files went allright, but when trying to analyse them, I get an error message about the SamReadGroupRecords List being null or empty.

Anybody has any suggestions?
KarinVL is offline   Reply With Quote
Old 11-13-2018, 05:21 AM   #2
Location: Norway

Join Date: Oct 2012
Posts: 20

You can add read group info to your bam-files using Picard's AddOrReplaceReadGroups ( You can also add it during alignment with the -R option to bwa.

More info about Read Groups here:
torben is offline   Reply With Quote
Old 08-29-2019, 01:11 PM   #3
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Location: Boston, MA

Join Date: Jul 2011
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Hi - did you find an answer? were you able to use Ion Reporter to analyze illumina data?
prat824 is offline   Reply With Quote

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