Hi!
I have a question related to cummeRbund 2. I want to generate plot which shows (only or also) the ensembleID for my genes and my transcripts. I tried to build the cuffData.db giving as gtf a gtf file with all the references (XLOC, TCONS, ensembl gene ID, ensembl transcript ID, TSS, etc), it built the db File and I can generate plots of dispersion and other quality plots, but when I head the gene.feature I don't see the ensembl IDs...so I'm trying to use the addfeatures function (giving as input always that gft file) but it takes ages and eventually makes R crush.
How can I add the ensembleID?
I have to say that the gft file that I'm giving as input is not the same used for generating the cuffdiff output files, should i use that one? or can I build the dbFile with that and then add feature with my "complete" gft File?
Thanks!
I have a question related to cummeRbund 2. I want to generate plot which shows (only or also) the ensembleID for my genes and my transcripts. I tried to build the cuffData.db giving as gtf a gtf file with all the references (XLOC, TCONS, ensembl gene ID, ensembl transcript ID, TSS, etc), it built the db File and I can generate plots of dispersion and other quality plots, but when I head the gene.feature I don't see the ensembl IDs...so I'm trying to use the addfeatures function (giving as input always that gft file) but it takes ages and eventually makes R crush.
How can I add the ensembleID?
I have to say that the gft file that I'm giving as input is not the same used for generating the cuffdiff output files, should i use that one? or can I build the dbFile with that and then add feature with my "complete" gft File?
Thanks!