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Search: Posts Made By: Brian Bushnell
Forum: Bioinformatics 09-28-2017, 10:27 AM
Replies: 347
Views: 184,308
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, 09:48 AM
Replies: 347
Views: 184,308
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: Bioinformatics 09-15-2017, 09:31 AM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
Actually, all the BBTools strip off the leading...

Actually, all the BBTools strip off the leading "-" so you can put as many of them as you want :)

This is a bug. Thanks for the report! It looks like BBDuk only removes reads under minlen or...
Forum: Bioinformatics 09-12-2017, 12:43 PM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
"maq=10" is to throw away really junky reads. ...

"maq=10" is to throw away really junky reads. The only way to really verify whether a setting is beneficial is to actually test it, unfortunately. But personally, I think "mbq=20" would be too...
Forum: Bioinformatics 08-14-2017, 10:25 AM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
Hi cuencam, It is currently not possible to...

Hi cuencam,

It is currently not possible to do this, other than discarding all reads that have any undefined (quality 0) bases with "maxns=0". I never saw a reason to discard all reads with a...
Forum: Bioinformatics 07-14-2017, 11:25 AM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
1) Generally, I consider Q20 too high for...

1) Generally, I consider Q20 too high for quality trimming and think it is probably detrimental to most analyses (not because removing low-quality sequence is bad, but because with Illumina sequence...
Forum: Bioinformatics 07-14-2017, 09:55 AM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
Oh, I should mention... I don't really touch...

Oh, I should mention... I don't really touch BBDuk2's code any more. I'm planning on deprecating it, since it's a lot of effort to keep two almost-identical programs in sync, and BBDuk2's only...
Forum: Bioinformatics 07-14-2017, 09:36 AM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
There was a bug in a previous version of BBDuk...

There was a bug in a previous version of BBDuk where minlength/maxlength were only checked if trimming occurred. That should be fixed in the latest version. What version are you using?
Forum: Bioinformatics 06-30-2017, 09:03 AM
Replies: 347
Views: 184,308
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 06-27-2017, 10:48 AM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
Hi Ksenia, This is always a tricky problem...

Hi Ksenia,

This is always a tricky problem when people rename the reads. However, it looks like in your case the file is interleaved (that's my guess from the read headers), and thus you should...
Forum: Bioinformatics 06-07-2017, 12:55 PM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
20000x * 15000bp / 150bp = 2 million reads, which...

20000x * 15000bp / 150bp = 2 million reads, which is plenty. 1000x * 15000bp /150bp = 100 thousand reads, which is insufficient. So, it depends. However, you can use the entire lane for...
Forum: Bioinformatics 06-06-2017, 02:20 PM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
I do not recommend extremely stringent...

I do not recommend extremely stringent quality-trimming prior to variant-calling (or most anything, for that matter). In general, it reduces mapping accuracy and increases various forms of bias;...
Forum: Bioinformatics 06-06-2017, 11:31 AM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
Since you have 5 different overlapping sections,...

Since you have 5 different overlapping sections, if you trim the primers all at once with no precautions, you will break your assembly into 5 segments since anything read overlapping a primer region...
Forum: Bioinformatics 05-18-2017, 11:16 AM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
Probably the one trimming more is better. ...

Probably the one trimming more is better. Geneious is probably trimming more by overlap because overlap trimming happens after adapter-sequence trimming, so if some adapter sequences are missing,...
Forum: Bioinformatics 05-17-2017, 02:08 PM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
No idea; those commands should be equivalent,...

No idea; those commands should be equivalent, unless the adapters.fa file is different. Can you post the full output of the command so I can see where the bases were lost? Also, you may want to add...
Forum: Bioinformatics 05-06-2017, 04:27 PM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
Haha :) The syntax would be: bbduk.sh...

Haha :)

The syntax would be:

bbduk.sh in1=R1.fq.gz in2=R2.fq.gz loglog loglogk=31 out=stdout.fq > /dev/null/

But, you don't need to specify anything, as the default is to not print anything...
Forum: Bioinformatics 05-05-2017, 11:19 AM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
Hi Brian, That's intentional. The 5th base...

Hi Brian,

That's intentional. The 5th base call is an N, which means the quality score should be 0 (!) not 2 (#). Some versions of Illumina software have bugs causing some Ns to be assigned...
Forum: Bioinformatics 04-18-2017, 02:10 PM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
BBDuk supports a sliding window; the flags...

BBDuk supports a sliding window; the flags "qtrim=w,4 trimq=15" will give similar behavior to Trimmomatic. But I don't recommend that; the Phred trimming method used by default is optimal, whereas...
Forum: Bioinformatics 04-18-2017, 10:08 AM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
The difference is primarily because you are...

The difference is primarily because you are quality-trimming to Q27, which is too high for almost any purpose. I'd suggest a command more like this:

bbduk.sh -Xmx8g...
Forum: Bioinformatics 04-12-2017, 03:35 PM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
Ah! Good eye... OK, so here's what's...

Ah! Good eye...

OK, so here's what's happening:

in=x.fq in=x.fq

In1 is set as x.fq. Then, in1 is set as x.fq again (you can do this as many times as you want; BBTools all just overwrite...
Forum: Bioinformatics 03-02-2017, 08:53 AM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
To be clear, I like to use "left" and "right"...

To be clear, I like to use "left" and "right" rather than 3' and 5'. In a fastq file, reads have a left and right end, so...

A read's adapter is to the left of its left end. It does not get...
Forum: Bioinformatics 03-01-2017, 02:55 PM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
Nextera adapters are much longer than what you've...

Nextera adapters are much longer than what you've posted, which I have listed as the "Nextera Transposon". Longer sequences are more specific. The reason I have so many Nextera sequences is that...
Forum: Bioinformatics 02-28-2017, 09:19 AM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
Hi Jake, "mix" is primarily for...

Hi Jake,

"mix" is primarily for error-correct via overlap (ecco) mode when you want both overlapping and non-overlapping pairs output in the same file. I don't recommend it for merging because...
Forum: Bioinformatics 02-27-2017, 10:22 AM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
The default minoverlap for "tbo" is 14bp, and the...

The default minoverlap for "tbo" is 14bp, and the default mininsert is 40bp, which are fine except for uRNA (which needs mininsert=17) or a handful of other rare uses.
Forum: Bioinformatics 02-26-2017, 04:28 PM
Replies: 347
Views: 184,308
Posted By Brian Bushnell
Hi Jake, BBDuk takes exponential time to...

Hi Jake,

BBDuk takes exponential time to process the reference when you increase the maximum number of substitutions. Specifically, allowing 3 substitutions with K=27 requires 82^3 or 551,368...
Showing results 1 to 25 of 104

 


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