thanks for your time,
I'm dealing with complete human genome data where I'm majorly focusing on repeat regions, but surprisingly i see so many repeat reads falling under supplementary reads ( chimeric ) this is the case in BWA & Dragen, but bowtie2 is dropping those locations where there is case of supplementary reads, so majority of repeat reads are dropping by bowtie2 and majority of reads are getting aligned by BWA & Dragen but most them are chimeric.
I wanted to spend good enough time to understand aligners mechanism while its is dealing with repeat reads, i'm just seeing the overall counts from this 3 aligners. but to pin point to repeat locations specific alignment, i want to choose best possible aligner among this 3 or any other aligner which gives good results. but what type of info will tell me that a particular aligner is doing good while aligning repeat reads.
How can i know accuracy of it, how can i validate whether the aligned location is right or not, and how to deal with chimeric reads, how to understand why aligner is generating so many chimeric reads.
I'm sorry if i'm confusing you, but mainly i'm very curious to understand about chimeric reads in different aligners results. how can we deal with chimeric reads when we dont want to drop those reads.
thanks you so much once again, i'm open for discussion anytime. i really appreciate your help.