Differences In The Cuffcompare Output When Using Annotations

Question

[upendrakumar.devisetty]

I have couple of questions regarding cufflinks/cuffcompare:

I found strange results when i compare the cufflinks with annotation and cuffcompare and cufflinks with no annotation and cuffcompare. Here are the results:

# with annotation:
[upendra_35@vm142-17 Denovo_stuff]$ cut -f3 cufflinks_out/cuffcompare_out.transcripts.gtf.tmap |sort|uniq -c
41003 =
7 c
1 class_code

# Without annotation:
[upendra_35@vm142-17 Denovo_stuff]$ cut -f3 cufflinks_out_no_annot/cuffcompare_out_no_annot.transcripts.gtf.tmap |sort|uniq -c
11935 =
6397 c
1 class_code
5014 e
562 i
16519 j
7226 o
1844 p
51 s
8169 u
624 x

Why is it that we only one class with cufflinks with annotation. I have already checked the annotation file and transcripts.gtf file and the chromosome names match. I believe the cufflinks without annotation might be true. Right?

The result above is based on 3 lanes of illumina data. Do you think we can increase the percentages of interesting classes (o and u) if you include more data?

Thanks in advance......