transcripts.gtf files size vs. merged.gtf

Question

[Xin]

Hi

I have two transcripts.gtf files which are outputs of cufflinks. One is 69.4 Mb and the other one is 38 Mb.

When I merge these files with their annotation file the merged.gtf file is 75 Mb. Why it is small in size? (69.4 + 38 = 107.4), so I mean the minimum size of merged file should be 107.4. Isn't it?

Answer 1

[Martombo]

did you merge them with cufflinks? if so, the transcripts that are common to both files will be present only once in the merged.gtf. that's what merging is for. also, counting the number of transcripts is more informative than looking at the size.

[Xin]

I see. Thank you very much.