multiple aligned reads

[Carmen Navarro]

Hi,

when I align reads to a reference with MosaikAligner, I get results that can be (among others): Uniquely or multiple aligned mates. I have understood reading the documentation that an "uniquely aligned mate" means  that a read has been aligned to a unique region in the reference genome.

My question is what does the output exactly mean for Multiple Aligned Mates. In the output file, it seems to me that there is only one alignment per read, but I am not quite sure. If I obtain only one alignment also for Multiple Aligned Mates, is it the best match for each read? Is there a way that I get all the positions to which these reads match?

Thanks in advance,

Carmen Navarro

[Wan-Ping Lee]

Hi Carmen,

You are right that each read would appear only once in the bam. The one in the bam is the best (according to MOSAIK's criteria). However, there is an option of MOSAIK to generate all the positions of alignments of a read. That is -om. Here I have a post on our website to talk about multiply-mapped alignments, http://blog.gkno.me/post/40766675028/capturing-multiply-mapped-alignments.

Best,

Wan-Ping

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Wan-Ping Lee
Postdoctoral Research Associate
Department of Biology, Boston College

Tel: +1 (617) 552-2922
wanpi...@bc.edu