Anybody know a best fit method for determining mask/indexes for the mouse genome? I saw on another post they recommended the 25 bp/50 bp sets from the manual supplementation for a 35 bp plant sample. I figured I could just apply the same masks to my own. I'm running both the 25 and 50 specified index sets right now. I imagine I might have to use 'btestindex' Any help is appreciated and thanks!
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Originally posted by JohnK View PostAnybody know a best fit method for determining mask/indexes for the mouse genome? I saw on another post they recommended the 25 bp/50 bp sets from the manual supplementation for a 35 bp plant sample. I figured I could just apply the same masks to my own. I'm running both the 25 and 50 specified index sets right now. I imagine I might have to use 'btestindex' Any help is appreciated and thanks!
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Originally posted by nilshomer View PostSince the genome size of mouse and human is close enough in size, you can use the indexes for human recommended in the manual. Of course, the polymorphism rate is ~10 times greater in mouse but that may be why you are using BFAST (?).
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Interpreting Btestindex Output?
Nils,
Below is the command and sample output of Btest index, I am guessing that the two way table has the sensitivity numbers, given the error model defined by row and column.
Can you expand on what BP:0,1:del,2i1,2i2 etc mean?
Is it one insertion of size 2 or 2 insertions of size 1 etc?
Also is there a way to get the cumulative answer (i.e after being filtered by all masks?)
$ btestindexes -a 1 -r 80 -A 0 -S 10000 -I 2 -M 8 -f maskset1
...MASKS IN BFAST FORMAT
1111111111111111
1011001101010101100111011001
11010101010011010010100101000111
1110101001101111101111
N Masks = 1
MM BP:0 1=del 2i1 2i2
0 1.000 1.000 1.000 1.000
1 1.000 1.000 1.000 1.000
2 1.000 1.000 1.000 1.000
3 1.000 1.000 1.000 1.000
4 1.000 1.000 0.999 1.000
5 0.999 0.995 0.994 0.992
6 0.994 0.978 0.975 0.975
7 0.976 0.942 0.937 0.933
8 0.936 0.890 0.882 0.875
:::::::::::::::::::::::::::::::::::::::::
:::::::::::::::::::::::::::::::::::::::::
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Originally posted by cdry7ue View Post
Can you expand on what BP:0,1:del,2i1,2i2 etc mean?
Is it one insertion of size 2 or 2 insertions of size 1 etc?
Also is there a way to get the cumulative answer (i.e after being filtered by all masks?)
Originally posted by cdry7ue View PostAlso do you have any mask suggestions vis a vis ion torrent ? (It may be moot at this point given the number of reads, but may be some day in the future.)
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