Question: Rockhopper to perform alignment and differential expression analysis
gravatar for brendarc
10 days ago by
brendarc0 wrote:

Hey everyone, Im quite new in bioinformatics, and because of that as I didn't have experience with comand line in biolinux, I choose to use Rockhopper ( after trimming ) to perform alignment, and all steps until differential expression analysis data. My question if anyone is using it, from result table, first, normalization data gave very high values, and i tried to calculate upper quartile, as they said, I couldnt get in the same values, second, I also couldnt understand when they calculate RPKM if they are using reads or fragments, since i have paired end data, and they have this option when u load your data. They explained that on RPKM calculation they use upper quartile, but they are not clear about the RPKM and expression values. I tried to calculate both "normal" RPKM and this other modificated and i can't get in the same values. If anyone could help me I will be really grateful. Thanks, Brenda

rna-seq • 94 views
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