RNAseq _generating tx2gene table and using kallisto output to run DEseq
1
0
Entering edit mode
@nupurdasgupta-14604
Last seen 6.3 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 • 1.2k views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 9 hours ago
United States

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

ADD COMMENT

Login before adding your answer.

Traffic: 786 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6