Hi All-
I'm using cufflinks to assemble transcripts with a Drosophila genome annotation file from refSeq (refFlat), cuffcompare to create a "_combined.gtf" file from multiple samples, and cuffdiff to detect differential expression between samples using the "_combined.gtf". I'm particularly interested in the tss_group files since these allow me to look at the behavior of individual transcription start sites between samples.
In general, everything seems to be working properly. My problem is that 10% of transcripts are missing from the tss_group files, despite the fact that these same transcripts have FPKM values, and they are present in the isoform, gene, and other cuffdiff output files.
My initial explanation was that the missing transcripts were removed because they overlap, but I've found many overlapping transcripts present in the tss_group files.
Has anyone encountered this/have any thoughts?
Thanks,
-Dan
I'm using cufflinks to assemble transcripts with a Drosophila genome annotation file from refSeq (refFlat), cuffcompare to create a "_combined.gtf" file from multiple samples, and cuffdiff to detect differential expression between samples using the "_combined.gtf". I'm particularly interested in the tss_group files since these allow me to look at the behavior of individual transcription start sites between samples.
In general, everything seems to be working properly. My problem is that 10% of transcripts are missing from the tss_group files, despite the fact that these same transcripts have FPKM values, and they are present in the isoform, gene, and other cuffdiff output files.
My initial explanation was that the missing transcripts were removed because they overlap, but I've found many overlapping transcripts present in the tss_group files.
Has anyone encountered this/have any thoughts?
Thanks,
-Dan
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