RNAseq _generating tx2gene table and using kallisto output to run DEseq
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@nupurdasgupta-14604
Last seen 4.4 years ago

I generated the Kallisto output files for a mouse dataset using ensemble database.EnsDb.Mmusculus.v79. Next I am trying to use the kallisto output for DESeq. To do so I need to generate the Tx2gene table for transcript to gene conversion. Used the following code.

biocLite("ReportingTools")
library("tximport")
library("readr")
library("ReportingTools")
library("AnnotationDbi")
library(ensembldb)
library(EnsDb.Mmusculus.v79)
txdf <- transcripts(EnsDb.Mmusculus.v79, return.type="DataFrame")
tx2gene <- as.data.frame(txdf[,c("tx_id", "gene_id")]) 

But failed to get the results.  I would also like to tun DESeq using the kallisto output. I  appreciate your thoughts and help.  
 

deseq annotate • 701 views
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@mikelove
Last seen 4 hours ago
United States

If there was an error please report the error and the code that produced the error.

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