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Old 12-11-2009, 02:41 PM   #5
Location: California

Join Date: Jul 2009
Posts: 46
Lightbulb SE novoaligned data to MAQ pileup?

Originally Posted by zee View Post
I've put some results for simulated data and the novo2maq conversion here for anybody who is interested.
However, some figures for real data should be more conclusive so these are just a preliminary.
So I aligned my Single-End illumina data with MAQ then took all the unmappable reads and aligned those with NovoAlign. Now I'm wondering if I should use the novo2maq function and combine the file with my file and then generate a consensus pile up from that


if I should write my own python script to take the Novo Native output and add that to my pileup file from MAQ. (should be rather straightforward)

My concern is how novo2maq transfers the information about indels within individual reads to MAQ and how MAQ outputs this indel data after aligning to the reference.

I have not seen this concern raised elsewhere and am wondering what you all think about my situation. What are the benefits to using novo2maq and maq to create the composite pileup versus generating it myself?


Update: I ran "novo2maq" then "maq pileup" and you lose the indel data in the novoalign Native format output. it seem to just output everything just to relative to offset start position of the mapping. I think i might make my own conversion tool...

Last edited by der_eiskern; 12-11-2009 at 04:10 PM.
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