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
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?
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).