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Old 01-16-2017, 09:09 PM   #1
sanchari24
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Location: india

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Default Making RNA-seq Data comparable

Hello,

I have rna-seq data from two different tissues collected at different stress conditions. I have performed adapter removal using Cutadapt and I have used TopHat for alignment to the reference genome. What is the ideal method to combine the read-counts from the different datasets ? Should I perform CuffDiff on individual stress-tissue dataset, extract the FPKM files from each of the experiments and merge them using some normalization method ? I need a way to normalize the read-counts across all the stress-tissue datasets because I want to construct co-expression network using RNA-seq data. Any suggestion will be very helpful. Thanks.
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