Hello,
I'm using ASpli to calculate DU and DE of 4 Arabidopsis thaliana's RNA-Seq samples, but when i get to the step of estimating differential gene expression and bin/junction usage, with the DUreport command, i get the following error:
The full command that I'm using is:
du <- DUreport( counts, targets, minGenReads=10, minBinReads=5 , offsetAggregateMode = c("geneMode", "binMode")[1])
counts and targets were successfully made:
targets
bam genotype time
Sample_231 sampleChr1-231.bam Con t0
Sample_231a sampleChr1-231a.bam Con t0
Sample_235 sampleChr1-235.bam Con t1
Sample_235a sampleChr1-235a.bam Con t1
Sample_236 sampleChr1-236.bam Mut t0
Sample_236a sampleChr1-236a.bam Mut t0
Sample_238 sampleChr1-238.bam Mut t1
Sample_238a sampleChr1-238a.bam Mut t1
counts
Object of class ASpliCounts
Gene counts: 9701 genes analysed. Access using countsg(object)
Gene RD: 9701 genes analysed. Access using rdsg(object)
Bin counts: 86494 bins analysed. Access using countsb(object)
Bin RD: 86494 bins analysed. Access using rdsb(object)
Junction counts: 1369 junctions analysed. Access using countsj(object)
What could be the problem? Is there a way for me to test the intermediate files created by the DUreport to go step by step and figure out what is going on?
Any help will be really appreciated! Thank you all in advance,
Hello, I'm using ASpli to calculate DU and DE of 4 Arabidopsis thaliana's RNA-Seq samples, but when i get to the step of estimating differential gene expression and bin/junction usage, with the DUreport command, i get the following error:
Error in avRdBin/gen.rdb : non-conformable arrays Calls: DUreport ... .DUReportBins -> .filterBins -> .filterByRdBinRATIO Execution halted
The full command that I'm using is: du <- DUreport( counts, targets, minGenReads=10, minBinReads=5 , offsetAggregateMode = c("geneMode", "binMode")[1])
counts and targets were successfully made:
What could be the problem? Is there a way for me to test the intermediate files created by the DUreport to go step by step and figure out what is going on?
Any help will be really appreciated! Thank you all in advance,
Cordially,
Fernanda Luz P Costa