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I think my runs of gigabuild and gigabayes are not working. I've been looking at the log files and it seems like I'm not locating any of my reads in my assembly, which seems a bit odd. I'm using 454 data and the ace file that Newbler produces. For reads, I used the sfftools and Pyrobayes to convert my reads to fasta and qual files and ran both of those through Gigabuild, but I don't think anything was written to the assembly. Does anyone have any insight into what might be the issue? I could just build the assembly through Mosaik and see if that works, but it's seems a bit odd that that would be the issue.
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I'm having the exact same problem. Did you find a solution? -
Any good reason why you don't use FreeBayes, the successor of "gigabayes"?
Maybe your problem just vanishes ..
AFAIK gigabayes is not part anymore of Mosaik Aligner
hth, SvenComment
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mestato,
To be honest, I gave up on Mosaik and moved on to something else since no one would get back to me. I got some initial responses, but I could figure out the issue. I was trying to use the Mosaik pipeline to improve calls and generate snps, but have gone over to using a pipeline with a more traditional mapping and samtools approach. Let me know if you have any questions as I can offer what limited information I have.
Cheers,
NateComment
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I did not even know FreeBayes existed, I'll give that and the samtools' mpileup a shot. Thanks for the advice!Comment
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