[Sheila]

masks for SOLiD paired-ends reads 35+50nt

See section 7.1.

Hi there,
I've gone through the Bfast manual and I found a suggestion for masks assuming reads of at least 50nt in section 7.1.2. The problem is that my paired reads do not have the same length (SOLiDv4, paired-end libraries not mate-pair libraries, they have different orientation), one has 35nt in length and the other one has 50nt. Do I need to use different masks in order to index the reference for reads with 35nt or it's OK if I use those masks suggested in the manual for 50nt reads also for 35nt reads?

Thanks in advance.

Best regards,

S.

[nilshomer]

Hi there,
I've gone through the Bfast manual and I found a suggestion for masks assuming reads of at least 50nt in section 7.1.2. The problem is that my paired reads do not have the same length (SOLiDv4, paired-end libraries not mate-pair libraries, they have different orientation), one has 35nt in length and the other one has 50nt. Do I need to use different masks in order to index the reference for reads with 35nt or it's OK if I use those masks suggested in the manual for 50nt reads also for 35nt reads?

Thanks in advance.

Best regards,

S.

Try the bfast+bwa code. BFAST will map the 50bp read, and BWA will map the 35bp read, then BFAST will merge the two. There are many discussions here about how to run bfast+bwa.

[Ramon Vidal]

I have question regarding the "masks" in the index. What are the masks and why do we need them? Thanks for the response!

This is a question that intrigues me for some weeks. Do you already have the answer for that? Anyone?

I have created the 10 mask for human genome (hg18). To run bfast with all 10 masks I only point to the prefix of the index right? Or somehow I have to run the bfast match for each one of the masks?

Thank you

[nilshomer]

This is a question that intrigues me for some weeks. Do you already have the answer for that? Anyone?

I have created the 10 mask for human genome (hg18). To run bfast with all 10 masks I only point to the prefix of the index right? Or somehow I have to run the bfast match for each one of the masks?

Thank you

That's right, it will find all of them for you. You can use "-i" to specify a subset, for example "-i 2-3,6,9-10".

[pengchy]

Hi,
I have found a potential error in the Table 1 of the bfast main manuscript (http://www.plosone.org/article/info:...l.pone.0007767). The M1 mask only has 18 "1", but the key size and key width both are 22. Is this a typo or my misunderstanding?

M1=111111111111111111 (k = 22, w= 22) M M M M

One more question:
I am working for a genome size two times the human and pair-end 100bp reads. Can I use the recommended mask that used for human pe50 data, or need I regenerate the mask set?

based on the function:

f <- function(L=50,k=18,G=2*3.2*1e+9,A=4){
  return((L-k+1)*(G/(A^k)))
}
f(L=100,k=22,G=2*7.2*1e+9,A=4) ## 0.06466507

The f = 0.06466507, which is less than 1. Is it mean that I can use the key size 22 and the recommended mask set? Thanks in advance.

[nilshomer]

See the recommended settings in the manual! Good catch on the typo.