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Forum: Bioinformatics 10-25-2017, 10:51 PM
Replies: 347
Views: 185,376
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: 347
Views: 185,376
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, 01:40 AM
Replies: 347
Views: 185,376
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 06-30-2017, 09:33 AM
Replies: 347
Views: 185,376
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: 347
Views: 185,376
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: 347
Views: 185,376
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,...
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