Hi guys.
I was just wondering about some peoples opinions on RNA-Seq aligning methods. Maybe I'm misunderstanding it but I would think that seed extend aligners like STAR are inherently better, since they are able to make a decision on if something is spliced or unspliced. (And have the added benefit of being more suitable for mapping to a combination of human and bacteria, if one was looking at a host-pathogen interaction or something). As opposed to exon first methods (like Tophat) which map reads continuously first then deal with the spliced alignments after (which I think would bias the reads to map continuously).
What do you think?
Here is a good nature methods review discussing it for those that are interested but don't know about aligners. http://www.nature.com/nmeth/journal/...d=NMETH-201106
I was just wondering about some peoples opinions on RNA-Seq aligning methods. Maybe I'm misunderstanding it but I would think that seed extend aligners like STAR are inherently better, since they are able to make a decision on if something is spliced or unspliced. (And have the added benefit of being more suitable for mapping to a combination of human and bacteria, if one was looking at a host-pathogen interaction or something). As opposed to exon first methods (like Tophat) which map reads continuously first then deal with the spliced alignments after (which I think would bias the reads to map continuously).
What do you think?
Here is a good nature methods review discussing it for those that are interested but don't know about aligners. http://www.nature.com/nmeth/journal/...d=NMETH-201106
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