Cuffcopmare: errors when using UCSC known genes

[mrfox]

Hi all,
I am trying to use cuffcompare (v0.9.2Beta) to compare my rebuilt transcriptome with UCSC known gene annotations. However, I got the error messages though I did obtain the combined.gtf and .tracking files eventually. Any explainations?
Thank you.

GFF Warning: discarded overlapping feature segment (40547903-40548425) for GFF ID uc007aug.1
.....
Warning: transcript uc008hap.1 discarded (structural errors found, length=261032).

Warning: found 10930 transcripts with undetermined strand.
Warning: found 139706 transcripts with undetermined strand.

[RockChalkJayhawk]

One of your annotation files is not correct in the placement of strand information. I would start there.

[mrfox]

Hi RockChalkJayhawk, thanks for your reply. Unfortunately, I do not quite understand what you are saying. Could you say more about that? The annotation I used was the standard GTF file of UCSC known genes. Thanks again.

[RockChalkJayhawk]

Use one of these GTFs and see if your problem is solved. But first you will need to modify it

awk '{print"chr"$0}' Ensemble.GTF > New.gtf

[mrfox]

I tried to use Ensemble annotation as reference and it does not have problem. However, I would like to use UCSC KNOWN GENES as reference. Did you have the same warning messages when you use known gene annotations? Thank you.

[RockChalkJayhawk]

Part of the problem is because the gene_id and transcript_id are all the same when you try to export from UCSC. Is there a reason you don't want to use the ENSEMBLE?

[mrfox]

I see.
In my mind, UCSC known genes include more annotations than Ensemble. I just want to make sure that the "new isoforms" reconstructed is truly new.