Question

Bowtie Accuracy

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11.7 years ago

Arpssss ▴ 40

I am experimenting with BowTie v 1 for various length reads (75 to 200 bp). Now, my task is to find it's throughput and accuracy. But, I can't understand how to find it's accuracy. Now, I was suggested to use an fully accurate tool and compare it to BowTie in-order to find accuracy. Can anybody help me, is there any other method (because that is really time consuming work) ? Or if I must have to compare BowTie with another tool, can anybody help me which tool I can use for above purpose. Thanks in advance.

NB: BowTie uses only substitution for finding mismatch.

bowtie alignment next-gen read • 2.4k views

ADD COMMENT • link updated 3.9 years ago by Biostar 20 • written 11.7 years ago by Arpssss ▴ 40

score 1 · Answer 1 · 2012-08-22

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11.7 years ago

Istvan Albert 100k

The answer is the same as to your previous question on this matter: http://www.biostars.org/post/show/47599/bowtie-inaccuracy-limit/

Look at the ROC curves by Heng Li: http://lh3lh3.users.sourceforge.net/alnROC.shtml

ADD COMMENT • link 11.7 years ago by Istvan Albert 100k

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No, I want to measure it for our databases. How much, false positive it gives ?

ADD REPLY • link 11.7 years ago by Arpssss ▴ 40

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generate the same curves for your data, the website contains the commands

ADD REPLY • link 11.7 years ago by Istvan Albert 100k