I wish to generate a diff_genes.txt file that includes the XLOC (no problem, includes it now) but also the gene name to make it easier to search for genes of interest.
The workflow breaks down after line 5:
R
library(cummeRbund)
cuff <- readCufflinks()
diffGeneIDs <- getSig(cuff,level="genes",alpha=0.05)
diffGenes<-getGenes(cuff,diffGeneIDs)
The last line produces the following error:
Error in sqliteExecStatement(conn, statement, ...) :
RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)
The .gtf file is from iGenomes for Homo_sapiens and does include the tss_id and p_id.
May I ask for suggestions to identify the problem and resolve it?
Thanks,
Cris
The workflow breaks down after line 5:
R
library(cummeRbund)
cuff <- readCufflinks()
diffGeneIDs <- getSig(cuff,level="genes",alpha=0.05)
diffGenes<-getGenes(cuff,diffGeneIDs)
The last line produces the following error:
Error in sqliteExecStatement(conn, statement, ...) :
RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)
The .gtf file is from iGenomes for Homo_sapiens and does include the tss_id and p_id.
May I ask for suggestions to identify the problem and resolve it?
Thanks,
Cris
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