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Forum: Bioinformatics 03-02-2017, 04:42 AM
Replies: 347
Views: 184,041
Posted By JVGen
Hi Brian, I always mix the placement of the...

Hi Brian,

I always mix the placement of the adapters up. I'm not sure what the location I'm referring to is called, but it is the sequence that is added by the transposase, and the location where...
Forum: Bioinformatics 03-01-2017, 04:25 AM
Replies: 347
Views: 184,041
Posted By JVGen
Thanks Brian. It doesn't look like clumpify has...

Thanks Brian. It doesn't look like clumpify has been built into Geneious as of yet, so I'll have to skip that trimming step.

Also, I was wondering why there were 71 sequences in the Nextera...
Forum: Bioinformatics 02-28-2017, 03:18 AM
Replies: 347
Views: 184,041
Posted By JVGen
Thanks Brian. If I intend to merge reads...

Thanks Brian.

If I intend to merge reads using BBMerge, should I only Adapter Trim, Merge, and then Trim with the other parameters?

I'm hoping to use "mix=t" with BBMerge, if downstream...
Forum: Bioinformatics 02-27-2017, 08:31 AM
Replies: 347
Views: 184,041
Posted By JVGen
Hi Brian, Thanks for the explanation. In...

Hi Brian,

Thanks for the explanation. In general, I have pretty high coverage which is why I had the trimming parameters set so strict - a minimum of ~1000x coverage in 150 x 2 PE reads (I'm...
Forum: Bioinformatics 02-26-2017, 11:15 AM
Replies: 347
Views: 184,041
Posted By JVGen
Hi Brian, I started using an HPC (36 CPUs @...

Hi Brian,

I started using an HPC (36 CPUs @ 3.5 GHz each & 60 GB RAM) to processes NGS data. I noticed that while using BBDuk, neither the RAM nor processors are being challenged, yet BBDuk takes...
Forum: Bioinformatics 11-07-2016, 11:02 AM
Replies: 347
Views: 184,041
Posted By JVGen
Hi Brian, You are correct. While the file...

Hi Brian,

You are correct. While the file names were correct in the program interface, upon export the "_" were introduced. I apologize for not opening up the fastq file in a texteditor to be...
Forum: Bioinformatics 11-07-2016, 10:32 AM
Replies: 347
Views: 184,041
Posted By JVGen
Hi Brian, I just recently started using...

Hi Brian,

I just recently started using BBDuk to adapter and quality trim. I then use the reads to assemble in Spades, but ran into an issue. The error correction software that Spades uses...
Forum: Bioinformatics 11-03-2016, 09:16 AM
Replies: 347
Views: 184,041
Posted By JVGen
Hey Brian. I heard back from Geneious. Turns...

Hey Brian. I heard back from Geneious. Turns out that I had to pair the reads before running BBDuk. After pairing I'm left with a single file in Geneious, though the reads have not been merged. ...
Forum: Bioinformatics 11-02-2016, 10:45 AM
Replies: 347
Views: 184,041
Posted By JVGen
Hi Brian, I'll report the issue to Geneious. I'm...

Hi Brian, I'll report the issue to Geneious. I'm using the "keep order" feature in Geneious. I've attached a screenshot. The check boxes and insert fields that Geneious created are nice for those...
Forum: Bioinformatics 11-02-2016, 10:05 AM
Replies: 347
Views: 184,041
Posted By JVGen
Thanks Brian. I found that the unequal read...

Thanks Brian. I found that the unequal read number following trimming was due to the " were being generated from read length cut-off. I was specifying a minimum read length of 30, but it was...
Forum: Bioinformatics 11-02-2016, 08:09 AM
Replies: 347
Views: 184,041
Posted By JVGen
BBDuk - Remove singletons?

Hi Brian,

I'm using BBDuk to adapter and quality trim Illumina reads that were prepped with the Nextera kit. I'm using the Plugin within Geneious, and I have a few questions:

1) I'm getting...
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