I work on RNA sequencing at the moment.
I've used tophat and cufflinks before, so now I'd like to do it in different way.
My new RNA-seq workflow is like below
BWA -> HTSeq-count -> TMM
However, I have no idea how to TMM after I finished BWA and HTSeq-count.
I've found that I have to use edgeR package in R and the function for TMM is calcNormFactors().
I've tried it already but there were some errors as I'm not much familiar with it.
Now I have about 10 bam files as a result of BWA, and 10 HTSeq-count results from that 10 bam files.
Each HTSeq-count result has two columns, one for gene symbols and the other for the counts.
(and last 4 rows are values about no feature, ambiguous, too low aQual, not aligned, alignment not unique)
1) How to TMM with HTSeq-count results.
2) What is the input format that I can make from those 10 HTSeq-count results for calcNormFactors() in R.