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Gene-Level Analysis
I'm planning an RNASeq study that I'm hoping will have multiple levels of use. In the short term I'm interested in looking at gene-level abundance. However, I'm planning experiments for the long term where I would use this data to look at isoform-level expression.
The difficulty I'm having is determining what workflow, if any, can be used to take paired-end reads and estimate gene level abundance.
I've looked into ERANGE, but it seems that it is designed for single end reads.
I also noticed that Cufflinks outputs a gene-level FPKM but I'm having a hard time finding any details about it. Has anyone used this and can anyone tell me what method is used to calculate this?
I would really appreciate any insight and suggestions for which tools/methods I should look into.
Thank you!
The difficulty I'm having is determining what workflow, if any, can be used to take paired-end reads and estimate gene level abundance.
I've looked into ERANGE, but it seems that it is designed for single end reads.
I also noticed that Cufflinks outputs a gene-level FPKM but I'm having a hard time finding any details about it. Has anyone used this and can anyone tell me what method is used to calculate this?
I would really appreciate any insight and suggestions for which tools/methods I should look into.
Thank you!
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