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Forum: Bioinformatics 10-13-2017, 11:14 AM
Replies: 87
Views: 14,586
Posted By Brian Bushnell
Hi Gopo, I don't particularly recommend...

Hi Gopo,

I don't particularly recommend Tadpole for diploid (or higher) genomes, as it has absolutely no capability of dealing with heterozygous sites. However, it's really fast, so even with a...
Forum: Bioinformatics 10-11-2017, 06:52 PM
Replies: 112
Views: 37,564
Posted By Brian Bushnell
As GenoMax says, trimming to Q30 is not...

As GenoMax says, trimming to Q30 is not beneficial before merging reads. BBMerge has some internal quality-trimming options, so it can try to merge, then quality-trim if it is unsuccessful, then try...
Forum: Bioinformatics 10-11-2017, 02:43 PM
Replies: 55
Views: 12,006
Posted By Brian Bushnell
Actually, "nodisk" does not work with BBSplit... ...

Actually, "nodisk" does not work with BBSplit... sorry! I'll clarify that in the documentation. It's not like it's impossible to make it work, but it would be pretty complicated; one of those...
Forum: Bioinformatics 10-11-2017, 01:48 PM
Replies: 112
Views: 37,564
Posted By Brian Bushnell
Hi Ashu, "Ambiguous" means there are...

Hi Ashu,

"Ambiguous" means there are multiple possible overlaps. For example, if read 1 and read 2 both end with "ACACACACACACACACACACAC", there are lots of possible overlap frames, none of which...
Forum: Illumina/Solexa 10-11-2017, 01:29 PM
Replies: 26
Views: 2,209
Posted By Brian Bushnell
I have not looked into that yet. Actually, I...

I have not looked into that yet. Actually, I don't even know if we are spiking PhiX into our Novaseq runs, but that rate is worth examining, after I find out whether there is actually any PhiX...
Forum: Bioinformatics 10-11-2017, 01:24 PM
Replies: 1
Views: 329
Posted By Brian Bushnell
I downloaded NA12878 from NIST, and they also...

I downloaded NA12878 from NIST, and they also have validated sets of small variations, but I didn't really find them all that useful. If anyone has validated CNV sets for those it would be NIST. ...
Forum: Illumina/Solexa 10-10-2017, 02:07 AM
Replies: 26
Views: 2,209
Posted By Brian Bushnell
It only works for applications that are not...

It only works for applications that are not sensitive to crosstalk. Personally, I would never multiplex samples of the same genus on a NovaSeq unless all libraries had dual unique barcodes. The...
Forum: Illumina/Solexa 10-09-2017, 06:59 PM
Replies: 26
Views: 2,209
Posted By Brian Bushnell
It's interesting to me that Illumina introduced...

It's interesting to me that Illumina introduced NovaSeq without accompanying adapter kits to enable a high degree of multiplexing. Their current 24-unique-index kit seems targeted at human...
Forum: Illumina/Solexa 10-09-2017, 03:06 PM
Replies: 26
Views: 2,209
Posted By Brian Bushnell
Oh, sorry, I meant OUR HiSeq machines :) Those...

Oh, sorry, I meant OUR HiSeq machines :) Those are 2000/2500/1T. In this specific case I was comparing it to a 2500 run.

To clarify, from isolate random fragment data downsampled to the same...
Forum: Bioinformatics 10-09-2017, 02:57 PM
Replies: 586
Views: 103,284
Posted By Brian Bushnell
Hi Gopo, Yes, I will add that (as an...

Hi Gopo,

Yes, I will add that (as an option). Is that common practice in other variant-callers? Note that callvariants.sh does currently have a "PF" (pass filter) field per sample, but I want to...
Forum: Bioinformatics 10-05-2017, 01:35 PM
Replies: 586
Views: 103,284
Posted By Brian Bushnell
reformat.sh has an option "underscore" which will...

reformat.sh has an option "underscore" which will change whitespace in sequence headers into underscores, if the extra information is important. Alternatively, as Genomax says, you can use...
Forum: Illumina/Solexa 10-05-2017, 01:24 PM
Replies: 26
Views: 2,209
Posted By Brian Bushnell
I don't know anything about the lab issues, but...

I don't know anything about the lab issues, but the sequence quality is good. Coverage exhibits slightly more bias than HiSeq for the same libraries. Using unique dual barcodes and performing...
Forum: General 10-05-2017, 01:19 PM
Replies: 14
Views: 1,512
Posted By Brian Bushnell
RAM is often the limiting factor in...

RAM is often the limiting factor in bioinformatics computing. I would not recommend buying a computer that you plan to use for bioinformatics with only 16 GB RAM unless it will be dedicated to some...
Forum: Bioinformatics 10-04-2017, 11:58 AM
Replies: 586
Views: 103,284
Posted By Brian Bushnell
1) I have not looked at Nanopore reads in...

1) I have not looked at Nanopore reads in several years now so I don't have any further experience in mapping them. But from what I read and hear the quality is gradually creeping upward (and my...
Forum: Bioinformatics 10-04-2017, 10:24 AM
Replies: 55
Views: 12,006
Posted By Brian Bushnell
The numbers of mapped reads do not add up to the...

The numbers of mapped reads do not add up to the same record in each case... it seems like the program is crashing and not processing all the reads, or else the input is different. The output is...
Forum: Bioinformatics 10-03-2017, 03:45 PM
Replies: 586
Views: 103,284
Posted By Brian Bushnell
Hi Dario and Genomax, I though I had gotten...

Hi Dario and Genomax,

I though I had gotten rid of that a while ago, but I guess not - I'll investigate and fix it. It's harmless and due to a race condition for a thread finishing after it was...
Forum: Bioinformatics 10-03-2017, 03:43 PM
Replies: 3
Views: 462
Posted By Brian Bushnell
Oh... in that case, speculation again, but it...

Oh... in that case, speculation again, but it sounds like it is for a scaffolding phase; essentially, a match of at least that long is required in a read to consider it as having come from that...
Forum: Bioinformatics 10-03-2017, 03:41 PM
Replies: 187
Views: 38,785
Posted By Brian Bushnell
Hi Dave, Thanks for the followup. I...

Hi Dave,

Thanks for the followup. I apologize for not getting back to you in a timely fashion, I'm pretty swamped currently!
Forum: Bioinformatics 10-02-2017, 04:26 PM
Replies: 55
Views: 12,006
Posted By Brian Bushnell
That's odd, if you are not intentionally...

That's odd, if you are not intentionally producing random assignments for sequences. Can you please post your full command line? Also, are the reads paired or unpaired?
Forum: Bioinformatics 09-28-2017, 11:27 AM
Replies: 281
Views: 60,916
Posted By Brian Bushnell
To clarify, I meant running Megahit (for example)...

To clarify, I meant running Megahit (for example) on the reads of the sample considered to be the background, then mapping the reads of the other sample to that assembly.
Forum: Bioinformatics 09-28-2017, 11:00 AM
Replies: 3
Views: 462
Posted By Brian Bushnell
I am not sure about IDBA, but Tadpole has a seed...

I am not sure about IDBA, but Tadpole has a seed kmer flag, and the meaning is:

Contigs are built starting with a single kmer, then extending it. However, only kmers with a sufficiently high...
Forum: Bioinformatics 09-28-2017, 10:55 AM
Replies: 586
Views: 103,284
Posted By Brian Bushnell
Yes, that's correct. This is especially...

Yes, that's correct. This is especially important for BBMerge, where insert size can only be computed from reads that overlap; so if the average calculated insert size is say 270bp for 2x150bp...
Forum: Bioinformatics 09-28-2017, 10:48 AM
Replies: 281
Views: 60,916
Posted By Brian Bushnell
You can find kmers that are shared between two...

You can find kmers that are shared between two samples like this (bearing in mind that it may take a lot of memory):

kcompress.sh in=a.fq.gz out=a_kmers.fa.gz
kcompress.sh in=b.fq.gz...
Forum: Illumina/Solexa 09-28-2017, 10:42 AM
Replies: 6
Views: 598
Posted By Brian Bushnell
Also, it's worth noting that Illumina base...

Also, it's worth noting that Illumina base quality is reduced with each successive cycle due to phasing drift. This phasing drift is reset when a new read begins starting at a primer location. ...
Forum: Bioinformatics 09-27-2017, 02:30 PM
Replies: 187
Views: 38,785
Posted By Brian Bushnell
Hi Dave, BBMap has some heuristics that may...

Hi Dave,

BBMap has some heuristics that may make it non-ideal for the situation with a large number of near-identical sequences, particularly when the reads don't map glocally well to any of them...
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