Cufflinks - 'u' Class Code - Consistently Returned

[AndrewCarpenter]

Steps taken:

KEY:
MCF_7_cDNA_fragments.sam (2X100 cDNA paired end aligned reads from MCF-7 cell line)

1. cufflinks -m 400 -p 10 -L MCF_7_transcript MCF_7_cDNA_fragments.sam

KEY:
transcripts.gtf (transcripts assembled from step 1)
Homo_sapiens.GRCh37.58.gtf ("reference" annotation from Ensembl)

2. cuffcompare -r Homo_sapiens.GRCh37.58.gtf transcripts.gtf

PROBLEM: The .tmap file lists all assembled transcripts as 'unknown intergenic transcripts' (class code "u")

Would this make sense if there wasn't any MCF-7 transcripts in the supplied reference file? Or how could this be?

Thanks for any help you can offer.

[AndrewCarpenter]

Cuffcompare Output Seems Incorrect

Steps taken:

KEY:
MCF_7_cDNA_fragments.sam (2X100 cDNA paired end aligned reads from MCF-7 cell line)

1. cufflinks -m 400 -p 10 -L MCF_7_transcript MCF_7_cDNA_fragments.sam

KEY:
transcripts.gtf (transcripts assembled from step 1)
Homo_sapiens.GRCh37.58.gtf ("reference" annotation from Ensembl)

2. cuffcompare -r Homo_sapiens.GRCh37.58.gtf transcripts.gtf

PROBLEM: The .tmap file lists all assembled transcripts as 'unknown intergenic transcripts' (class code "u")

Would this make sense if there wasn't any MCF-7 transcripts in the supplied reference file? Or how could this be?

Thanks for any help you can offer.

[nat]

Hi there.

I have the same problem with the latest version of Human Ensembl reference file.
(Homo_sapiens.GRCh37.60.gtf). I have added 'chr' in front of each chromosome number (beginning of each line) - as this was required when I did previous Cufflinks analysis with Homo_sapiens.GRCh37.55.gtf.

Cufflinks analysis worked well with the v55 of the reference file, but only see 'u' matches with the .60 version of the file. The only formatting difference I see between the two files is spaces between fields instead of tabs as in the v55 file. I have tried editing the file so the v60 file has tabs too - but this didn't help, in fact Cufflinks couldn't read the reference file.

Have you managed to solve your problem?

Cheers

[zun]

the difference between reference and gtf file

Hi,everyone

I had the same probrem that the cuffcompare output .tmap file had only 'u'.

I just resolved this to make chromosome names　between reference.gtf and my gtf file from cufflinks equal.

I hope this will help you