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Search took 0.05 seconds. Search: Posts Made By: Brian Bushnell
Forum: Bioinformatics Today, 09:43 AM
Replies: 9
Views: 879
Posted By Brian Bushnell
I would appreciate it, but please don't feel...

I would appreciate it, but please don't feel obligated. As long as I'm cited, I'll be happy :)
Forum: Bioinformatics Today, 09:00 AM
Replies: 9
Views: 879
Posted By Brian Bushnell
If that's a hexaploid, then presuming the primary...

If that's a hexaploid, then presuming the primary peak is the 6x homogeneous peak, the coverage is too low to see the haploid heterozygous peak, which would be at around 2.5x and indistinguishable...
Forum: Illumina/Solexa Yesterday, 07:38 PM
Replies: 9
Views: 503
Posted By Brian Bushnell
I have now partially analyzed a non-failed...

I have now partially analyzed a non-failed NovaSeq run. The quality is almost as good as HS2500, but not quite. So it's extremely good. Also, the quality drops much less for each additional cycle,...
Forum: Bioinformatics 07-10-2017, 02:21 PM
Replies: 9
Views: 879
Posted By Brian Bushnell
Visually, that looks like a very obvious haploid...

Visually, that looks like a very obvious haploid to me, with median coverage at ~16x and genome size of ~700Mbp for the unique stuff (using SUM(B8:B28) from your spreadsheet) and a couple hundred Mbp...
Forum: Bioinformatics 07-10-2017, 08:54 AM
Replies: 9
Views: 879
Posted By Brian Bushnell
The estimate is provided for convenience, but the...

The estimate is provided for convenience, but the accuracy is not guaranteed since it has to guess the peak locations, peak limits, and ploidy of the organism. It can be somewhat more accurate if...
Forum: Bioinformatics 07-07-2017, 08:49 AM
Replies: 8
Views: 430
Posted By Brian Bushnell
Oh, I see. I normally use the term "unique...

Oh, I see. I normally use the term "unique kmers" where he uses "distinct kmers", and "singleton kmers" or "depth-1 kmers" where he uses "unique kmers".
Forum: Illumina/Solexa 07-06-2017, 08:34 AM
Replies: 9
Views: 503
Posted By Brian Bushnell
NovaSeq looks promising. I'm not done analyzing...

NovaSeq looks promising. I'm not done analyzing the data yet; for our first run read 2 had lighting failures, but read 1 was very accurate. It has other issues, though, like barcode crosstalk.
...
Forum: Illumina/Solexa 07-06-2017, 12:42 AM
Replies: 9
Views: 503
Posted By Brian Bushnell
Illumina knows this, but they do not like to...

Illumina knows this, but they do not like to broadcast it, since they are trying to kill off their older platforms and sell newer platforms. So you will not get this kind of information from their...
Forum: Bioinformatics 07-05-2017, 10:32 PM
Replies: 8
Views: 430
Posted By Brian Bushnell
I can only think of two kmer counts... total,...

I can only think of two kmer counts... total, and unique. So, it seems like they may have a new category that I have not heard of, or there might be a misunderstanding. Please post the results of...
Forum: Bioinformatics 07-05-2017, 10:32 PM
Replies: 8
Views: 430
Posted By Brian Bushnell
I can only think of two kmer counts... total,...

I can only think of two kmer counts... total, and unique. So, it seems like they may have a new category that I have not heard of, or there might be a misunderstanding. Please post the results of...
Forum: Bioinformatics 07-05-2017, 08:52 PM
Replies: 8
Views: 430
Posted By Brian Bushnell
I don't use that term because I find it...

I don't use that term because I find it confusing. But I assume the authors mean, by "distinct kmers", the total number of counted kmers, whether unique or not. In my example, that would mean...
Forum: Illumina/Solexa 07-05-2017, 11:02 AM
Replies: 9
Views: 503
Posted By Brian Bushnell
You should go back to the company in one of these...

You should go back to the company in one of these cases:

1) The data is so bad you can't use it without compromising your experiment.
2) The data is usable, but bad enough that it might affect...
Forum: Bioinformatics 07-05-2017, 10:54 AM
Replies: 2
Views: 361
Posted By Brian Bushnell
Is this question in the context of...

Is this question in the context of high-throughput sequencing? Or do you just mean, in general, you want to study mitochondrial and you have no data yet?
Forum: Bioinformatics 07-05-2017, 10:46 AM
Replies: 8
Views: 430
Posted By Brian Bushnell
Consider "AAAAAA". When counting 3-mers, there...

Consider "AAAAAA". When counting 3-mers, there are 4 of them. But there is only one unique 3-mer: "AAA".
Forum: Bioinformatics 06-30-2017, 09:03 AM
Replies: 245
Views: 51,017
Posted By Brian Bushnell
Actually! I kind of dislike config files because...

Actually! I kind of dislike config files because I find them annoying. So nothing in BBTools requires them. But it does in fact support them, because sometimes they are convenient... particularly...
Forum: Bioinformatics 06-30-2017, 08:05 AM
Replies: 6
Views: 406
Posted By Brian Bushnell
I only had a chance to try it on one file, and it...

I only had a chance to try it on one file, and it worked fine in that case, but that's not a very robust test... can you send me the file you're using?

What you have posted might be enough to...
Forum: Bioinformatics 06-29-2017, 10:23 AM
Replies: 6
Views: 406
Posted By Brian Bushnell
What a coincidence, I have a script which does...

What a coincidence, I have a script which does just that in the BBMap package!

phylip2fasta.sh in=file.phylip out=file.fasta
Forum: Bioinformatics 06-28-2017, 10:01 AM
Replies: 6
Views: 420
Posted By Brian Bushnell
The problem is not so much the fraction of data...

The problem is not so much the fraction of data that is discarded, but rather, the bias - Illumina read quality is affected by sequence content, so a high quality-trimming or quality-filtering...
Forum: Bioinformatics 06-28-2017, 09:45 AM
Replies: 6
Views: 420
Posted By Brian Bushnell
I disagree with the part about quality-trimming. ...

I disagree with the part about quality-trimming. There is at least one published study indicating trimming to high levels like Q20 is generally detrimental to alignment, which agrees with my...
Forum: Illumina/Solexa 06-27-2017, 06:34 PM
Replies: 4
Views: 301
Posted By Brian Bushnell
You can usually compare data qualitatively if it...

You can usually compare data qualitatively if it was aligned by the same version of the same aligner, using the same reference.

You cannot usefully compare data quantitatively if:

1) The...
Forum: Illumina/Solexa 06-27-2017, 12:52 PM
Replies: 4
Views: 296
Posted By Brian Bushnell
Overloading shouldn't have any impact on flow. ...

Overloading shouldn't have any impact on flow. Flow problems are typically caused by machine-specific fluidics issues (clogged nozzles, etc), I believe.
Forum: Illumina/Solexa 06-27-2017, 11:32 AM
Replies: 4
Views: 301
Posted By Brian Bushnell
Yes, it could be any of those! Normally a bam...

Yes, it could be any of those! Normally a bam file's size is most closely related to the coverage, but the contents can vary considerably based on all of those factors - some aligners produce...
Forum: Bioinformatics 06-27-2017, 11:26 AM
Replies: 6
Views: 3,312
Posted By Brian Bushnell
You can also use BBMap's filtervcf.sh like this: ...

You can also use BBMap's filtervcf.sh like this:

filtervcf.sh in=original.vcf out=varCHR.vcf contigs=Chr01,Chr02,Chr03,Chr04,Chr05,Chr06,Chr07,Chr08,Chr09,Chr10

...assuming those chromosome...
Forum: Bioinformatics 06-27-2017, 11:22 AM
Replies: 2
Views: 429
Posted By Brian Bushnell
The peak-calling and ploidy estimation in...

The peak-calling and ploidy estimation in KmerCountExact are not very sophisticated, but I certainly expect them to do a better job than that! To my eye this is a very obvious diploid; not sure why...
Forum: Bioinformatics 06-27-2017, 11:05 AM
Replies: 2
Views: 327
Posted By Brian Bushnell
SPAdes documentation seems to indicate that the...

SPAdes documentation seems to indicate that the distribution of insert size is important to some of its heuristics, but I think coverage is more important... also it's a multi-kmer assembler so you...
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