I am analyzing RNASeq data using a Tuxedo pipeline. For the most part, the RNA sequences seem to align with known genes in the correct orientations.
A number of putatively new genes have been discovered, however. In the output GTF file, though, some of these new genes are not assigned to either the sense or the antisense strand, i.e. column 7 contains a "." instead of + or - sign.
Does anyone know why this might be the case? This seems to happen for the new genes but not the already known genes.
In the Cufflinks part of the analysis, I used the --GTF-guide option with a GFF3 file of exon locations that I downloaded from Flybase. I also used
--upper-quartile-norm --min-intron-length 5
A number of putatively new genes have been discovered, however. In the output GTF file, though, some of these new genes are not assigned to either the sense or the antisense strand, i.e. column 7 contains a "." instead of + or - sign.
Does anyone know why this might be the case? This seems to happen for the new genes but not the already known genes.
In the Cufflinks part of the analysis, I used the --GTF-guide option with a GFF3 file of exon locations that I downloaded from Flybase. I also used
--upper-quartile-norm --min-intron-length 5
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