Bioscope(diBayes) for SOLiD~need help

[SOLiDance]

Hi,I major in Molecular Bio,and what i am doing now need the SOLiD platform.
But I'm totally a green hand in Bioinfo stuff~ Today I got one problem, Maybe someone familiar with the Bioscope (Life Tech) can help me out ?
The diBayes tool in Bioscope pipeline is used to find SNPs.In the Life Tech's Bioscope Guide, about the Reference genome,it's said so:"Note: When you run the SNPs tool, you must use a different reference than the one used for mapping" sadly I only have one Ref version and don't know the reason for a different one~ It's getting more confusing after I read the diBayes Manual--Nothing said about Ref, No rule~
anybody know what's going on?
THANK U VERY MUCH!!

[mbblack]

Either your documentation has an error, or you misread it. In my BioScope 1.3 manual (page 194) it clearly says "Note: When you run the SNPs tool, you must use the same reference that was used for mapping." (that's a direct copy and paste). Since your BAM output from the mapping is based on that same file, only that would work.

[SOLiDance]

Either your documentation has an error, or you misread it. In my BioScope 1.3 manual (page 194) it clearly says "Note: When you run the SNPs tool, you must use the same reference that was used for mapping." (that's a direct copy and paste). Since your BAM output from the mapping is based on that same file, only that would work.

Yeah ! Thanks a lot!! In fact, I couldn't find the manual for Bioscope 1.3 ver while using it,still with the April 2010 Ver(maybe 1.2?) Just hope won't have any more error~
Hmm~SO GLAD~

[westerman]

It would be strange to have one reference for mapping and another one for SNP calling. Although now that I am working with the Illumina pipeline I find that I need the reference in two different forms -- squashed and non-squashed (unless I am missing something in the manual.)

Anyway back to SOLiD. You still need a 'cmap' file for some of the pipelines. This file relates the chromosomes names and order to individual chromosome files.

[SOLiDance]

Thanks for your info~
yesterday I encountered with new trouble. Later, we found it's VERY important to make sure that *.fa files have same order in CMAP and BAM. After fixed the script to get new CMAP, the run finished successfully.