Dear Biostars,
I want to find a way to search for reads that have reverse complements inside a library from a RIP-seq experiment.
I have found this related question: [Question: Finding complementarity between mRNA and rRNA using BLAST][1]
but nucleotide blast seems to be a bit different now.
Current blastn searches for reverse complement alignments too?
Is there a package that I could do it in R?

thank you in advance


  [1]: https://www.biostars.org/p/197164/
One option is `bedtools intersect` or `intersectBed` which can be run on two bam files.

    intersectBed -a shortReads.bam -b longReads.bam -S -bed

The -S flag will force the **opposite** strandedness (as opposed to the `-s` flag that forces same strandedness). You'll want to play with the `-f` flag that requires the fraction of A that must be overlapped (the default is 1bp, you may want to raise `-f  1.0` to require the entire short read overlaps the long read).