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Mapping mRNAs to MAGs/Genomes

Software to use dependent on data quality and RNA read length - mine is only 50bp - this is a "small RNA sequence" but does not actually come from a "small RNA"

Going to attempt using BBMap's "seal.sh" for mapping and generation of RPKM values.

Looks like seal.sh can map and produce RPKM values and also split the reads into bins? - How to format reference for these cases?

For mapping to a genome assembly, split into bins with genes?

seal.sh in=reads.fq *.fa stats=sealstats.txt rpkm=sealrpkm.txt ambig=random

For splitting reads into bins?

seal.sh in=reads.fq *.fa pattern=out_%.fq outu=unmapped.fq ambig=all refnames=t