gigabayes no output

[shaohua.fan]

Hi, all,
I met a problem when I use the gigabayes to detect SNPs from my cDNA assembly.

gigaBuild produced the gig file, but the output of the gigaBayes only includes some parameters information, NO snp information is presented.

anybody met this problem before?

[skingan]

I'm having this problem too. I am working with both a 454 dataset and a solexa dataset. I am running each of the chromosomes separately and I can get gigaBayes to work for all but 1 of the chromosomes for the 454 data, but none for the solexa data. Very strange. Any ideas?
Sarah
[email protected]

[jgibbons1]

5 months later and I'm having the same problem.

Have you figured out what was causing this yet? If so, I would GREATLY appreciate hearing about your solutions.

-John

[alessandra85]

I' am having this problem too. I am working with 454 dataset, but now that this is not working, I don't know what to do for finding SNPs. Do you have any solution? I would really aperecciate if you can help me!!

Thanks, Alessandra

[shaohua.fan]

Hi all,

I found the solution for using GigaBayes.

1st. use MIRA to assemble the raw reads. Then follow the suggestions/steps :

http://www.freelists.org/post/mira_talk/RE-Re-Inconsistent-unpadded-reads-length-in-ACE-file

please notice that the 2nd step caf2phrap -caf mira_out_unpadded.caf -fasta mira_out_reads.fasta -clip will only generate 2 files

mira_out_reads.fasta
mira_out_reads.fasta.qual

so in the 3rd step, gigaBuild --ace mira_out.ace --gig mira_out.gig --fd mira_out_reads.fasta --fq mira_out_reads.fasta.qual

you can use the ace file from MIRA directly.

Hope I have explained clearly to you. Keep posting if you have any question.

[alessandra85]

Thanks a lot!! it works great!!

But I have another question, now that I have discover some SNPs from my file, someone knows how from the gigabayes file, find if the SNPs are synonymous or no synonymous with any other program...

[shaohua.fan]

One thing you can do, what i am doing, is to blastx those contigs with SNPs. The blastx process can be termed as a ORF prediction. You can calculate , if within the ORF, the distance of SNP position to the start of the hit position, then divided by 3.

[alessandra85]

gigabayes information

Hi everybody

1. I got the log file from the SNPs output, and I was wondered if someone knows what is the menanig of calls. I got something like this

SNP 37 CALLS T(258.5) C(228.2) -(38.3) PSNP 1

I take that like the probability of having a SNP in that position. I was wondering if I can use that to get the allelic frequency T=(258.5*100)/(T+C+-)

2. Gigabayes has a ploidy paramenter, what do I use if my organism is poliploid? I used the 2 parameter haploid and diploid and there is a big difference between both of them. I got few SNPs with diploid parameter.

Thanks in advanced.