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
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
Comment