I am afraid I don't understand what you are looking at there. Are 'u' and '.' the only class codes you got in the .tracking file? Because that would rather suggest that the chromosome names do not match at all between the reference annotation and the input sample files (the chromosome IDs in the first column should follow the same naming convention, e.g. it shouldn't be 'chr1' in the GTF with the transfrags and '1' in the reference annotation file).
However in that case I don't get this statement:
What other categories? In the attached table picture I only see 'u' and '.' codes listed, and a summary 'Total transfrags' row, which makes me think there are no other categories / class codes. Sorry for being a little confused here about your questions.
Also, I suppose in order to compare the class code distribution in different samples, you were in fact looking at the .tmap files, not the .tracking file as you said, is that right? Because you mentioned you ran cuffcompare with 4 GTF files as input -- was that one cuffcompare run with all 4 files at once, or it was 4 different runs?
However in that case I don't get this statement:
All of the other categories are consistent across the board.
Also, I suppose in order to compare the class code distribution in different samples, you were in fact looking at the .tmap files, not the .tracking file as you said, is that right? Because you mentioned you ran cuffcompare with 4 GTF files as input -- was that one cuffcompare run with all 4 files at once, or it was 4 different runs?
Comment