I am following along with the de-novo transcript analysis tutorial here. I have been using collections to organize the data as I go (1 collection for Megakaryocyte data and 1 for G1E data).
The collections were not a problem until I needed to run featureCounts() on the alignment files from all 4 samples (the 2 MegaK replicates with the 2 G1E replicates). It does not appear that featureCounts() will allow you to select multiple collections for analysis (ie. it only allows me to choose either the MegaK collection, or the G1E collection, but not both). I also cannot seem to figure out how to ‘unpack’ the collections into individual files so that I can run all four files together.
Any help on either 1) running two collections together or 2) ‘unpacking’ the collections so that I can submit the individual files together, would be greatly appreciated.