Best software to use to annotate a .bam file? How to map to multiple references when first output is .bam?

Question

[agm123]

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?

[GenoMax]

1. You will need to retrieve the fastq reads from BAM file if you want to realign them. This can be done by using samtools fastq command or reformat.sh from BBMap suite.
2. What do you mean by annotate? You could get a GTF file for miRNA and use that to count the number of reads mapping to known miRNA's.