Replicates error in CummeRbund package in R

[Pinal]

Dear All,

I am analyzing RNAseq data to study DEGs in two diffrent conditions. i don't have any replicate for my samples. tophat->cufflinks->cuffdiff pipeline is completed and now i want to plot graphs using cummeRbund. while creating a database using readCufflinks package i am getting following error.

Creating database E:/cuff_out/cuffData.db
Reading Run Info File E:/cuff_out/run.info
Writing runInfo Table
Reading Read Group Info E:/cuff_out/read_groups.info
Writing replicates Table
Error in sqliteSendQuery(con, statement, bind.data) :
rsqlite_query_send: could not execute: UNIQUE constraint failed: replicates.rep_name


Can anyone please help me to solve this.?

[blancha]

What is the content of E:/cuff_out/read_groups.info?
What command was used to run Cuffdiff?
Also, perhaps not necessary, were there any error messages during the Cuffdiff run?

[Pinal]

thank for your reply blancha

Read_groups.info contains...

file condition replicate_num total_mass norm_mass internal_scale external_scale
control_tophat_out/accepted_hits.bam control 0 3.25226e+07 3.85494e+07 0.83201 1
test_tophat_out/accepted_hits.bam treated 0 4.569e+07 3.85494e+07 1.20191 1

cuffdiff was run with default command. along with two accepted_hits.bam file, human genome reference and GTF was there as input. i also used -u (rescue method for multi-reads.

cuffdiff was completed successfully.

[blancha]

Sorry, I don't know the answer.
Looks correct to me.
Other than suggesting to update CummeRbund If you have an ancient version, older than 2.7.3, I don't have any solutions to propose to this specific problem.

[Pinal]

thank for your reply blancha