BWA Mismatch

[ron128]

Arggggggggggh! l ast chance for someone to save my life, because unless i get a definitive answer, i am going to blast my brains off on this one! How do you set a mismatch option for paired end alignment in BWA.? I was looking up the forum and was driven nuts by all the options and various parameters. I never ended up with a one mismatch alignment in the end. Can someone give me the definitive parameters for one mismatch in BWA? prettty pleaaaase? i promise lots of cookies to be couriered to anyone who helps me out on this

[xied75]

-n 1
(waiting for the cookies)

[ron128]

http://seqanswers.com/forums/showthread.php?t=3917

I went through this thread and tried what davetang suggested, using simulated reads. Turns out he is right. Its not just the n option which defines the mismatch

[xied75]

That thread is 2010, with a much older version of BWA. What's wrong with -n 1, show some example?

[ron128]

Oh k been a while since my last post. sorry i could not reply earlier as i dont have access to a decent computer mainframe. I need to book my slot to run my computations. SO anyways i tried doing what was suggested, with n-1 and l-10000 effectively to disable seeding, and I am still scratching my head here.

Can anyone let me know how if there is a best hit criteria? Apparently I was lead to believe that the default option in BWA i.e. where we do not specify any parameters while using the aln option in sampe, is a "best hit" option which generates the "best" alignment, i.e. an alignment from all different alignments which has optimal read alignment. Looks like I need to study alignment in depth to better solidify my knowledge.

I had generated an alignment using these default options and i found that a certain no of reads i.e. X reads were aligning. Now when i use the n-1 option which is alowing one mismatch, in theory i should have gotten Y no reads aligning, where Y>X but alas I am getting the exact oppposite.

Thanks for all the help till now. ANd yes i think you deserve your cookies.