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Search: Posts Made By: boulund
Forum: Bioinformatics 04-15-2018, 10:54 AM
Replies: 8
Views: 3,313
Posted By boulund
I noticed that I missed the name0= argument to...

I noticed that I missed the name0= argument to sketch.sh that changes the name. Great! :)

I wrote a quick Python script that takes the output from comparesketch.sh and produces a heatmap...
Forum: Bioinformatics 04-14-2018, 06:33 AM
Replies: 8
Views: 3,313
Posted By boulund
What would be the optimal way to use these...

What would be the optimal way to use these sketching tools if I want to make metagenome sample comparisons similar to what e.g. Sourmash (http://sourmash.readthedocs.io/en/latest/) can do? My first...
Forum: Bioinformatics 11-07-2017, 01:54 AM
Replies: 212
Views: 57,200
Posted By boulund
Hi, just want to make sure I'm not missing...

Hi, just want to make sure I'm not missing anything here, but randomreads.sh cannot produce metagenomes according to a specific profile, right? I only find information about it drawing random numbers...
Forum: Bioinformatics 10-25-2017, 10:51 PM
Replies: 304
Views: 82,060
Posted By boulund
Hi! Is it possible to get the various...

Hi!

Is it possible to get the various quality histograms for both before and after e.g. trimming with BBDuk in a single run, or do I need to run BBDuk it twice to produce metrics for before and...
Forum: Bioinformatics 09-28-2017, 10:32 PM
Replies: 304
Views: 82,060
Posted By boulund
Ok, that's interesting. Our current approach was...

Ok, that's interesting. Our current approach was just that; assembly of the background sample with Megahit, and then mapping the sample to be filtered against the background assembly to remove...
Forum: Bioinformatics 09-28-2017, 10:14 PM
Replies: 650
Views: 132,616
Posted By boulund
Hi, thanks for that excellent response! I'm one...

Hi, thanks for that excellent response!
I'm one of the authors of a BBMap module for the MultiQC (http://multiqc.info/) bioinformatics log aggregation/summarization tool, and we'd love your...
Forum: Bioinformatics 09-28-2017, 01:40 AM
Replies: 304
Views: 82,060
Posted By boulund
Hi, I got the idea to use BBDuk as a tool to...

Hi,

I got the idea to use BBDuk as a tool to filter out kmers that are shared between two samples. Is this a good idea? It's metagenomics, and the concept is that one sample is representing the...
Forum: Bioinformatics 09-28-2017, 01:14 AM
Replies: 650
Views: 132,616
Posted By boulund
Hi, I have a question about the...

Hi,

I have a question about the PercentOfPairs output found in the insert size histogram output (ihist). What does it mean, percent of pairs? Is it the proportion of read pairs where an insert...
Forum: Bioinformatics 09-06-2017, 09:05 PM
Replies: 650
Views: 132,616
Posted By boulund
Oh, that was easy. Thanks a lot for your quick...

Oh, that was easy. Thanks a lot for your quick response, both of you. Sorry for not spotting that option!




The command I used was simple: statswrapper.sh in=assembly_1.fasta...
Forum: Bioinformatics 09-06-2017, 06:49 AM
Replies: 650
Views: 132,616
Posted By boulund
Hi, I have a question about statswrapper.sh....

Hi,

I have a question about statswrapper.sh. It says in the help text description that it supposedly runs stats.sh on multiple assemblies to produce one output line per file, but I only get a...
Forum: Bioinformatics 06-30-2017, 09:33 AM
Replies: 304
Views: 82,060
Posted By boulund
Hi, thanks for your reply! I understand your...

Hi, thanks for your reply!

I understand your sentiment. I actually agree with you on the annoyance on config files for the most part, but just stumbled upon the config-file features of BBTools...
Forum: Bioinformatics 06-30-2017, 08:18 AM
Replies: 304
Views: 82,060
Posted By boulund
Yes, naturally. Thanks for the help, but I think...

Yes, naturally. Thanks for the help, but I think I'm not making myself entirely clear. :)

I was envisioning using a config file to contain all the standard parameters I always want to use,...
Forum: Bioinformatics 06-30-2017, 04:58 AM
Replies: 304
Views: 82,060
Posted By boulund
Hi, Is it possible to include some kind of...

Hi,

Is it possible to include some kind of filename wildcard in config files somehow?
I'd like to output base quality, stats, and some other histogram data for each invocation of bbmap/bbduk,...
Forum: Bioinformatics 01-26-2017, 01:21 AM
Replies: 650
Views: 132,616
Posted By boulund
Perfect, thank you! :)

Perfect, thank you! :)
Forum: Bioinformatics 01-25-2017, 05:45 AM
Replies: 650
Views: 132,616
Posted By boulund
I think so too, it feels natural considering the...

I think so too, it feels natural considering the memory usage profile of BBMap :) .
Forum: Bioinformatics 01-25-2017, 04:21 AM
Replies: 650
Views: 132,616
Posted By boulund
How does BBMap make use of an index on disk? I'm...

How does BBMap make use of an index on disk? I'm on a shared cluster system and I'm essentially wondering if BBMap performs a nice single pass of the index to read it into memory, or if it performs a...
Forum: Bioinformatics 01-24-2017, 10:54 PM
Replies: 19
Views: 5,534
Posted By boulund
Thanks for your really swift reply Brian! ...

Thanks for your really swift reply Brian!

Sorry, I'm not being very clear...
I'm really wondering whether bbcountunique is still useful somehow as a tool for quantifying the saturation of a...
Forum: Bioinformatics 01-24-2017, 12:57 AM
Replies: 19
Views: 5,534
Posted By boulund
But could this approach still be used with e.g....

But could this approach still be used with e.g. metagenomics data to get some kind of feeling for if the sequencing depth is deep enough? I guess what I'm really asking is whether you think it would...
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