Hello,
I have been working with a couple different Drosophila annotation files for an RNAseq experiment. I was wondering if within the Drosophila community there was a preferred annotation file that is being used. The main focus of the project is differential expression. I have used dmel-all-r5.9.gff from flybase and genes.gtf in the drosophila build5.3 from NCBI.
I'm using these annotations with htseq-count with tophat2 .bam files as the input. I find a huge difference in count numbers between the two files, with nearly 10 million reads given a "no_feature" tag in the dmel-all-r5.9.gff file compared to only about 300,000 in the genes.gtf file.
Any advice you can offer would be much appreciated!
Chris
I have been working with a couple different Drosophila annotation files for an RNAseq experiment. I was wondering if within the Drosophila community there was a preferred annotation file that is being used. The main focus of the project is differential expression. I have used dmel-all-r5.9.gff from flybase and genes.gtf in the drosophila build5.3 from NCBI.
I'm using these annotations with htseq-count with tophat2 .bam files as the input. I find a huge difference in count numbers between the two files, with nearly 10 million reads given a "no_feature" tag in the dmel-all-r5.9.gff file compared to only about 300,000 in the genes.gtf file.
Any advice you can offer would be much appreciated!
Chris