cufflinks warning messages

[pinki999]

Hi,

I am using cufflinks to analyze the RNA-seq data. When I used ./cufflinks -N sample.sorted.bam I did not get any warning messages. Also, I did not get any warning messages when I used Homo_sapiens.GRCh37.61.gtf as the annotation file but all the FPKM values in genes.expr were 0.

But when I downloaded a gtf file from UCSC genome browser with assembly:hg18 and track: Refseq Genes, I am getting several warning messages like:

Warning: duplicate GFF ID: NR_029462
Warning: duplicate GFF ID: NM_001145466

Warning: transcript NM_024813 discarded (structural errors found, length=89211)

I get such errors for quite a number of transcripts.

Could any one of you shed some light on this?

Thanks,
Pinki