Hi everyone, I'm doing a transcriptome of zebrafish, 2 replicates for each condition of 3 conditions. Trimmed adapters and low quality, fastq groomed, and mapped with tophat using the reference genome. So assembled with cufflinks every replicate with genome annotation and reference, but when i tried to merge with cuffmerge I got an error, a friend said to me to redo cufflinks step without annotation and reference, and use reference and anotation on cuffmerge step. And it worked, but when i try cuffdiff with the cuffmerge transcripts I got an error, tried use cuffcompare instead of cuffmerge but got error on cuffdiff too (final of log error below) and i dont know what is it, i tried precompute expressions with cuffquant and use de cxb instead of tophat bams, got error too, someone can help ?
Reading ./gene_exp.diff Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "integer"' Calls: readCufflinks ... make.db.names -> .valueClassTest -> is -> <Anonymous> In addition: Warning message: attributes are not identical across measure variables; they will be dropped Execution halted