Hi all,
I have a fastq file containing reads from an Illumina NextSeq smallRNA sequencing, a fasta file representing the genome (it is composed by about 33000 sequences with length 18-35 nts), the index and a bed file with coordinates of the genome.
After adapters trimming the reads are 18-35 nt of length...and I mapped the resulting fastq to the fasta (using either star or bowtie).

Now I would like to keep ONLY the reads that 100% overlap the features presents in the fasta (I mean that the reads need to be aligned end-to-end to the feature, and the feature has to be covered entirely by the read....so no nucleotides uncovered)...if not, read has to be discarded.

It seems star aligner and bowtie have no options to do it.....

I have any idea on how to proceed....could someone help me ?

Thank you a lot!