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-   -   Issue with StringTie--not picking up reference gene IDs (http://seqanswers.com/forums/showthread.php?t=79470)

sanchari24 12-07-2017 12:48 AM

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 ?

Thanks


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