Question: Rockhopper to perform alignment and differential expression analysis
0
gravatar for brendarc
10 days ago by
brendarc0
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
ADD COMMENTlink written 10 days ago by brendarc0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1164 users visited in the last hour