Question: Recommended program for evaluating aligner sensitivity
0
gravatar for fiona.newberry
2.1 years ago by
fiona.newberry80 wrote:

I am assessing 6 aligners and need to make roc curves to show the sensitivity and specificity of the aligners.

Can anyone recommend a program that can assess the resulting reads? I was going to use dwgsim_eval but my reads were not simulated with dwgsim. I need to extract false positive and true positive rates for the roc curves

Thanks

bwa smalt soap stampy bowtie2 • 702 views
ADD COMMENTlink modified 2.1 years ago by mark.ziemann1.2k • written 2.1 years ago by fiona.newberry80
2
gravatar for mark.ziemann
2.1 years ago by
mark.ziemann1.2k
Australia/Mebourne/Geelong/Deakin
mark.ziemann1.2k wrote:

You could try Teaser.

ADD COMMENTlink written 2.1 years ago by mark.ziemann1.2k

Thank you. Could I use Teaser if I already generated the simulated reads? I am reading about it and it appears that it can only be used with the reference genome (simulates reads itself).

ADD REPLYlink written 2.1 years ago by fiona.newberry80

I would go with Teaser if I were you. But if you have a specific need outside of the scope of it you could simulate the reads yourself (use ART) then use bedtools/awk to determine whether reads were mapped near the expected position with the expected orientation. This will at least get you some sensitivity/specificity data that you can use in ROC plots.

ADD REPLYlink written 2.1 years ago by mark.ziemann1.2k

Teaser looks good. Apparently I can provide my own simulation. Thanks again

ADD REPLYlink written 2.1 years ago by fiona.newberry80
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