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Originally posted by 11xinqi View PostHi, 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
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Originally posted by Azazel View PostI 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.
If you know why cufflinks give out so many one exon transcript, please tell me . thank you
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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.
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[cufflinks] every transcript is only one exon
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.
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