Weirdly enough, featureCounts requires input BAM/CRAM to be sorted by read name instead of coordinate (in order to keep paired reads together).
If coordinate-sorted input is given, featureCounts first sorts the input stream by name using huge temporary files (because they are uncompressed SAM!).
Since task_fq2cram.sh should be keeping the "unsorted" BAM/CRAM file around, that one should be served directly to featureCounts in this mini-RNAseq pipeline.
Weirdly enough, featureCounts requires input BAM/CRAM to be sorted by read name instead of coordinate (in order to keep paired reads together).
If coordinate-sorted input is given, featureCounts first sorts the input stream by name using huge temporary files (because they are uncompressed SAM!).
Since
task_fq2cram.shshould be keeping the "unsorted" BAM/CRAM file around, that one should be served directly to featureCounts in this mini-RNAseq pipeline.