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Old 04-20-2017, 11:25 AM   #1
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Location: USA

Join Date: Jun 2015
Posts: 5
Default retain barcodes in the output file after isoseq analysis in SMRTlink

I have a sample set that were barcoded uniquely for each sample. After we did IsoSeq analysis with barcoding options in SMRTlink, I obtained reads that were sorted by barcodes. However, on further analysis I need to "clean up"/ remove reads that were not correctly binned due to incomplete barcodes.

I can no longer see the barcodes on these reads anymore to check if that is an issue as final barcoded fastq files have reads trimmed of barcodes. Any Idea how to get the reads sorted out without trimming the barcodes?
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