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Dear all,
I am using a standard DEXSeq analysis for differential expression work. My gene annotations come straight form Ensembl. However I am having a few questions re the use of DEXSeq. My main concern is that, because of the large number of transcripts that link to the same gene, there seems to be extensive "cutting" of the gene regions.
I am interested for example in a mouse gene called Tardbp with only 8 exons. But when I create the gff file for DEXSeq count computation, I end up with 33 distinct regions. I guess that this sort of splitting is bound to reduce the power at some point, as each region has a lower read count. Does anyone have a view re the appropriate balance here? Is there a point in using perhaps less sophisticated gene annotations in order to increase the power of the DEXSeq analysis? Is there a recommended gene definition file?
Lastly, and this is less important, the transcripts are not showing up anymore under the DEXSeq standard plots, whatever options I set. They used to though... I cannot even figure out there DEXSeq pulls the transcript information from. I suspect this is an annotation problem of some sort, and my naming of exons may not be what it should. But if someone has a suggestion, I will take it.
Thanks,
Vincent
I am using a standard DEXSeq analysis for differential expression work. My gene annotations come straight form Ensembl. However I am having a few questions re the use of DEXSeq. My main concern is that, because of the large number of transcripts that link to the same gene, there seems to be extensive "cutting" of the gene regions.
I am interested for example in a mouse gene called Tardbp with only 8 exons. But when I create the gff file for DEXSeq count computation, I end up with 33 distinct regions. I guess that this sort of splitting is bound to reduce the power at some point, as each region has a lower read count. Does anyone have a view re the appropriate balance here? Is there a point in using perhaps less sophisticated gene annotations in order to increase the power of the DEXSeq analysis? Is there a recommended gene definition file?
Lastly, and this is less important, the transcripts are not showing up anymore under the DEXSeq standard plots, whatever options I set. They used to though... I cannot even figure out there DEXSeq pulls the transcript information from. I suspect this is an annotation problem of some sort, and my naming of exons may not be what it should. But if someone has a suggestion, I will take it.
Thanks,
Vincent