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.
1 answer
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
generate the same curves for your data, the website contains the commands
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