I have aligned miRNA sequences to a human reference. Many miRNA pipelines suggest aligning to the human reference, then to a database such as miRBase. I have two general questions. I have read many papers that state mapping to human genome then to miRBase. My question is how exactly is this done? In methods I have not seen this level of detail.
1) The output to alignment is a .bam file. How can this output be used(as input) to perform a sequential mapping to miRBase? My understanding is that FASTQ/A files are input to alignment.
2) If I want to annotate the .bam file I already have, what specific software can I use that will take this and a GTF or GFF file as input and produce as output annotated sequences?