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-   -   Using Ion Reporter for data from other platforms (http://seqanswers.com/forums/showthread.php?t=84555)

KarinVL 09-11-2018 06:32 AM

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?

torben 11-13-2018 05:21 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 01:11 PM

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


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