I used the STAR aligner to align a bunch of single-cell fastq files and then subsequently ran RSEM for quantification. Now I have 96 sets of RSEM outputs, and I want to combine all these (preferably TPM columns) into a single matrix.
I searched online, but could not find an easy way of doing it. The trinity denovo transcriptome building tool may have a perl script that is applicable, but then I didn't understand how to use it for this purpose. RSEM's "rsem-generate-data-matrix" seems simple to use, but then the filenames have to be manually given as inputs, which would be very cumbersome in my situation and the command wouldn't probably accept 96 files.
So, anybody here knows a better way to do this? Is there a ready-made tool for this? I would like to pick the TPMs, if possible.
Any help would be appreciated!
Thanks a lot.