BFAST index set for murines

[JohnK]

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!

[nilshomer]

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!

Since 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 (?).

[JohnK]

Since 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 (?).

Affirmative- I'm using BFAST primarily for concordance with SOLiD data analysis. It'd be nice to figure out btestindex... I'll keep looking at the manual and maybe I'll get it down.

[cdry7ue]

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
:::::::::::::::::::::::::::::::::::::::::
:::::::::::::::::::::::::::::::::::::::::

[cdry7ue]

Also 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.)

[nilshomer]

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?)

There is no manual for this and I will not support it, but read the supplemental materials in the original BFAST paper for more info. Use the recommended masks in the manual's appendix if you are unsure.

Also 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.)

For BFAST, I would recommend using a smaller key size and width, but this is at the cost of run time. If you are unsure of what this means or how to tune this, use the recommended masks. Two other mappers that may be useful for Ion Torrent are SHRiMP2 or TMAP (available and documented on the Ion Torrent website).