I've successfully gotten scatter plots, etc. in cummeRbund, but then when I try to actually dig into the data (trying to see if individual transcripts match the patterns we've seen previously with qPCR, convincing myself and my PI that this RNAseq is working) I don't see any gene ID in the cuff_diff files.
I don't have a .gtf file of my genome, only a .gff file and it sounds beyond my abilities to change it to a .gtf, and cuffmerge only takes .gtf files for annotation. You can run cuffmerge without a "-r <ref.gtf>" but if I do this, will I never have annotations in my later files?
Can I use cuffcompare with my .gff annotations to get gene names in the cuff_diff output?
Also, if I don't have specific gene annotations in my cuffdiff file, then what are showing up as my points in the cummeRbund scatter plots?
Thanks for your help,
Anna
I don't have a .gtf file of my genome, only a .gff file and it sounds beyond my abilities to change it to a .gtf, and cuffmerge only takes .gtf files for annotation. You can run cuffmerge without a "-r <ref.gtf>" but if I do this, will I never have annotations in my later files?
Can I use cuffcompare with my .gff annotations to get gene names in the cuff_diff output?
Also, if I don't have specific gene annotations in my cuffdiff file, then what are showing up as my points in the cummeRbund scatter plots?
Thanks for your help,
Anna
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