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Old 09-11-2018, 07:32 AM   #1
KarinVL
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Location: Netherlands

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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?
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Old 11-13-2018, 06:21 AM   #2
torben
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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
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