Tweet
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.
-
-
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
-
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
-
I did not even know FreeBayes existed, I'll give that and the samtools' mpileup a shot. Thanks for the advice!Comment
-
I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
Comment