RNASeq analysis using featureCount and EdgeR I am using a pipeline (bam -&gt; featurecount-&gt; EdgeR) to do some RNASeq analysis of several groups and sub-groups. For example, I have the following dataset with two types (T1 and T2) and T1 has three groups G1, G2 and G3, T2 has G5 and G6 groups. I would like to find TPM numbers, fold-change and FDR for all the genes and Groups.
Type Group SRA_Run#
T1   G1.   &lt;some SRA ids e.g. SRR123456, SRR112233&gt;
T1   G2.   &lt;some SRA&gt;
T1.  G3.   &lt;some SRA&gt;
T2.  G5.   &lt;some SRA&gt;
T2.  G6.   &lt;some SRA&gt;

I have individual BAM files generated for each SRA Run. I also individual read counts from featureCount for each SRA Run. I was not sure if I need to merge individual read counts for each group or run featureCount using all bam files of a group at once. Does it make any difference in  the analysis that follows.
I also would like to know if I can run EdgeR at once for all the types and groups at once for doing differential gene expression for each group of Type 1 (T1) against every other group of Type 2 (T2). I am bit stuck at this point how to proceed. Any help would be appreciated.
It makes no difference if you process the BAM files one at a time with featureCounts or all together, except that it changes how you have to read the files into R.
You can supply edgeR with lists of contrasts to have it compute fold-changes and p-values for. Please have a look at the edgeR user guide for examples.