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Old 12-07-2017, 12:48 AM   #1
sanchari24
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Location: india

Join Date: Jan 2017
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Default Issue with StringTie--not picking up reference gene IDs

Hello, I am using StringTie for RNA-seq analysis and want to use DESeq for differential gene expression analysis.

After running the command for creating ballgown input files, I used PrepDe.py to extract the gene_count matrix. It is not picking up most of the gene annotations and using default StringTie IDs. Is there a way to work around the problem ?

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