Using Ion Reporter for data from other platforms

KarinVL · 09-11-2018, 07:32 AM

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?

torben · 11-13-2018, 06:21 AM

You can add read group info to your bam-files using Picard's AddOrReplaceReadGroups (https://broadinstitute.github.io/pic...laceReadGroups). You can also add it during alignment with the -R option to bwa.

More info about Read Groups here: https://software.broadinstitute.org/...le.php?id=6472

prat824 · 08-29-2019, 02:11 PM

Hi - did you find an answer? were you able to use Ion Reporter to analyze illumina data?

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09-11-2018, 07:32 AM	#1
KarinVL Junior Member Location: Netherlands Join Date: Sep 2018 Posts: 1	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?

11-13-2018, 06:21 AM	#2
torben Member Location: Norway Join Date: Oct 2012 Posts: 19	You can add read group info to your bam-files using Picard's AddOrReplaceReadGroups (https://broadinstitute.github.io/pic...laceReadGroups). You can also add it during alignment with the -R option to bwa. More info about Read Groups here: https://software.broadinstitute.org/...le.php?id=6472

08-29-2019, 02:11 PM	#3
prat824 Junior Member Location: Boston, MA Join Date: Jul 2011 Posts: 2	Hi - did you find an answer? were you able to use Ion Reporter to analyze illumina data?