As already mentioned in the title, I'm looking for pre-computed matrix of gene counts for both human and mouse.
For example, in this paper "Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment" they only provide matrice of TPM for human mapped rnaseq here.
I know most of the time people use Xenome or Disambiguate to remove potentially mouse reads but they can be also informative of the mouse tumor environment.
Also Fastq can be tricky to access because data is related to patient and sequence are under dbgap access....
Does someone as heard of a website with this kind of resource like (Recount or Digital Expression Explorer 2) could provide but with mapping for both species in this PDX context.
Also sometimes it can be cell lines that have been used engrafment in mouse PDX so fastq can be more easy to access...
