[cufflinks] every transcript is only one exon

[Azazel]

I have a problem with cufflinks, all the transcripts which I assemble always consist of just one exon in the resulting GTF file!

I started with fasta files, aligned them with BLAT. Converted the output to bed12. Converted the bed12 to bam with bamToBed of samtools, and sorted.

Then I used cufflinks and get a GTF file. In that GTF file, the assembled transcripts look good, but each transcript is just one exon long: there is no intron-exon structure, altough it *is* still in the bed12 file, and there are no alternative splicing pathways generated.

I am a beginner with cufflinks. Any help appreciated. Thanks.

[Amative]

Hi Azazel, were you able to figure out you problem ?

Thanks!

[AJenkins]

I am having this same problem, is there any reason why?

[dpryan]

All of the splicing information would get lost in the process of converting to BED format. There's no possible way that pipeline could ever not produce only single-exon loci.

[11xinqi]

I have a problem with cufflinks, all the transcripts which I assemble always consist of just one exon in the resulting GTF file!

I started with fasta files, aligned them with BLAT. Converted the output to bed12. Converted the bed12 to bam with bamToBed of samtools, and sorted.

Then I used cufflinks and get a GTF file. In that GTF file, the assembled transcripts look good, but each transcript is just one exon long: there is no intron-exon structure, altough it *is* still in the bed12 file, and there are no alternative splicing pathways generated.

I am a beginner with cufflinks. Any help appreciated. Thanks.

Hi, Azazel, have you figure out what is the problem about transcripts with only one exon? I kind of met such problem. In my case, I used tophat + cufflinks to detect the differential expression. I have 3000 differentially expressed genes. 2800 genes of them are single-exon genes. The other 200 genes are multiple-exons gene.

If you know why cufflinks give out so many one exon transcript, please tell me . thank you

[dpryan]

Hi, Azazel, have you figure out what is the problem about transcripts with only one exon? I kind of met such problem. In my case, I used tophat + cufflinks to detect the differential expression. I have 3000 differentially expressed genes. 2800 genes of them are single-exon genes. The other 200 genes are multiple-exons gene.

If you know why cufflinks give out so many one exon transcript, please tell me . thank you

The cause of your issue will be completely different. Please start a new thread.

[11xinqi]

The cause of your issue will be completely different. Please start a new thread.

What you do mean about starting a new thread. would you please talk a little bit more?

[dpryan]

What you do mean about starting a new thread. would you please talk a little bit more?

That means to post a new question (not a reply to a previous question) on this forum, giving details about the commands you used.