Hi
I'm starting to use bfast and I have some doubts about some indexing parameters.
When indexing do I have to do it with the 10 spaced seed? I know this is to create different indexes to find the best CAL.
Which number should I use for -w parameter and why?
This is an example. Should it be run such way? 10 times? Can it be runed less than 10 times? Is it fixed (I mean it can be runned at a maximum of 10 times with the prefixed -m I show below or I could run it 11 times being the 11th such like '10001')
Thanks for your time.
I'm starting to use bfast and I have some doubts about some indexing parameters.
When indexing do I have to do it with the 10 spaced seed? I know this is to create different indexes to find the best CAL.
Which number should I use for -w parameter and why?
This is an example. Should it be run such way? 10 times? Can it be runed less than 10 times? Is it fixed (I mean it can be runned at a maximum of 10 times with the prefixed -m I show below or I could run it 11 times being the 11th such like '10001')
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1111111111111111111111" -w 14 -i 1
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111110111011101010010101101111" -w 14 -i 2
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1011110101101001011000011010001111111" -w 14 -i 3
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "10111001101001100100111101010001011111" -w 14 -i 4
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "11111011011101111011111111" -w 14 -i 5
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111111100101001000101111101110111" -w 14 -i 6
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "11110101110010100010101101010111111" -w 14 -i 7
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111101101011011001100000101101001011101" -w 14 -i 8
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1111011010001000110101100101100110100111" -w 14 -i 9
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1111010010110110101110010110111011" -w 14 -i 10
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111110111011101010010101101111" -w 14 -i 2
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1011110101101001011000011010001111111" -w 14 -i 3
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "10111001101001100100111101010001011111" -w 14 -i 4
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "11111011011101111011111111" -w 14 -i 5
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111111100101001000101111101110111" -w 14 -i 6
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "11110101110010100010101101010111111" -w 14 -i 7
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111101101011011001100000101101001011101" -w 14 -i 8
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1111011010001000110101100101100110100111" -w 14 -i 9
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1111010010110110101110010110111011" -w 14 -i 10
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