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Old 04-25-2016, 07:18 AM   #1
KateShepard
Junior Member
 
Location: UK

Join Date: Apr 2016
Posts: 5
Default biological replicates cuffmerge?

Dear forum,

I have 5 RNA-seq biological replicates and wish to examine the expression levels of specific genes/pathways of interest (high/low/not expressed) (no differential expression analysis).

I have mapped all samples to the appropriate ref genome/annotation using tophat2 and have assembled transcriptomes using cufflinks.

My question is now should I merge the 5 cufflinks assemblies together using cuffmerge, and use the merged assembly as my master transcriptome?

Also, is there a good tool/approach to visualise the variability between my biological replicates?

Thank you for your advice
Kate
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