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Old 08-28-2013, 10:54 AM   #1
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Join Date: Aug 2013
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Default Drosophila Annotation Files


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!

hardyc is offline   Reply With Quote

annotation, drosophila, gtf annotation file, htseq count, rnaseq

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