I am looking for the DNA methylation, specifically inside small RNAs; piRNA. I am mapping BS-seq reads on the genome with bismark. From the user guide of bismark, it maps reads uniquely on the genome, which mean it reports first read with best score and discard rest of the alignment and if a read mapping to multiple location with same score it will discard all such reads.
Typical command for obtaining uniquely mapped reads from bismark
~/Software/Bismark-0.22.3/bismark GenomePATH/Original_Genome/ --bowtie2 -p 10 -1 Methylation_reads/Sample1_R1.fq.gz -2 Methylation_reads/Sample1_R2.fq.gz --bam -o Sample1
Since, I am interested in piRNA only which may have multiple source in the genome (one piRNA coded from different location of genome), I wanted to take all mapped locations in consideration. Can you suggest what changes I have to make in bismark command. After reading bismark user guide I am confused because I could not able to find relevant parameter.
Also, please let me know if this approach is correct, if not what may be best approach for this.