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I was wondering why you have used RUM and not Tophat for your alignments. By the way have you tried Fanse?

Nucleic Acids Res. 2012 Jun;40(11):e83. doi: 10.1093/nar/gks196. Epub 2012 Feb 29.
FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads.
Zhang G, Fedyunin I, Kirchner S, Xiao C, Valleriani A, Ignatova Z.

Hi Antón,

There are many short read aligners each with their own merits and advantages.

RUM, like TopHat, uses Bowtie. RUM also uses BLAT to align to the genome.

There are several reasons why we use RUM for our alignments in GWIPS-viz.

One reason is that RUM outputs unique mappers (reads that map to only one location in the genome) separately from non-unique mappers. We currently display unique mappers only, although we do hope to incorporate non-unique mappers into the profiles.

Another reason is that RUM outputs coverage plots which we can incorporate directly into GWIPS-viz.

RUM outputs other files which are useful (such as junction calling, etc). For more details on RUM, see

If users have feedback on short read aligners, such as FANSe which you mentioned, that would be very interesting to hear.

Thanks Audrey
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