Question: Bowtie Accuracy
0
gravatar for Arpssss
8.3 years ago by
Arpssss40
Arpssss40 wrote:

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.

read next-gen bowtie alignment • 1.7k views
ADD COMMENTlink modified 6 months ago by Biostar ♦♦ 20 • written 8.3 years ago by Arpssss40
1
gravatar for Istvan Albert
8.3 years ago by
Istvan Albert ♦♦ 85k
University Park, USA
Istvan Albert ♦♦ 85k wrote:

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 COMMENTlink written 8.3 years ago by Istvan Albert ♦♦ 85k

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

ADD REPLYlink modified 8.3 years ago • written 8.3 years ago by Arpssss40

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

ADD REPLYlink written 8.3 years ago by Istvan Albert ♦♦ 85k
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