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Forum: Metagenomics 03-01-2015, 01:10 PM
Replies: 2
Views: 4,526
Posted By MicroBio
Sorry this is a super late response, but maybe it...

Sorry this is a super late response, but maybe it can help somebody in the future.

It can really depend on the kinds of bacteria you plan on finding. Different variable regions are better for...
Forum: Metagenomics 03-01-2015, 01:06 PM
Replies: 3
Views: 2,208
Posted By MicroBio
We use DeconSeq for human contamination removal....

We use DeconSeq for human contamination removal. It has an online application as well as a stand-alone version so you can try it out online before spending the time installing it. Unfortunately it...
Forum: Bioinformatics 09-23-2013, 07:10 AM
Replies: 3
Views: 2,741
Posted By MicroBio
Thanks nickloman, I used IDBA-UD. I'll look...

Thanks nickloman,

I used IDBA-UD. I'll look into whether or not it will give me that output like you mentioned. Otherwise I will go ahead and re-align the reads and deal with it from there. I...
Forum: Bioinformatics 09-23-2013, 05:42 AM
Replies: 3
Views: 2,741
Posted By MicroBio
Question Filtering Contigs by Coverage

Hi all,

I have a dataset where I assembled sequences into contigs and would now like to filter the contigs by coverage. My goal is to remove the contigs with low sequence coverage so that I can...
Forum: Illumina/Solexa 09-02-2013, 04:46 PM
Replies: 11
Views: 8,025
Posted By MicroBio
Thanks ScottC!

Thanks ScottC!
Forum: Illumina/Solexa 08-20-2013, 02:30 PM
Replies: 11
Views: 8,025
Posted By MicroBio
Okay cool! Is that on the MiSeq or HiSeq?

Okay cool! Is that on the MiSeq or HiSeq?
Forum: Illumina/Solexa 08-20-2013, 01:36 PM
Replies: 11
Views: 8,025
Posted By MicroBio
Thanks JackieBadger! What kind of coverage do...

Thanks JackieBadger! What kind of coverage do you get on the mtDNA genomes? Also, you are using Nextera and not Nextera XT right (although my understanding is that they are pretty similar)?
Forum: Illumina/Solexa 08-20-2013, 12:28 PM
Replies: 11
Views: 8,025
Posted By MicroBio
Question Problems using NexteraXT with mitochondrial DNA

Hi all,

I just prepared a NexteraXT library of mitochondrial DNA for a collaborator. Although they purified the mitochondrial DNA (removed genomic DNA), the sequencing results from the MiSeq...
Forum: De novo discovery 04-06-2013, 05:32 PM
Replies: 3
Views: 1,520
Posted By MicroBio
Going off of what severin was saying, do you...

Going off of what severin was saying, do you think you could use a loose mapping constraint to pick out some regions of interest (areas where your reads map to other species), and then perform a...
Forum: Bioinformatics 04-04-2013, 04:16 PM
Replies: 1
Views: 1,132
Posted By MicroBio
I would use -max_target_seqs.

I would use -max_target_seqs.
Forum: Illumina/Solexa 04-04-2013, 03:15 PM
Replies: 5
Views: 4,959
Posted By MicroBio
In our [somewhat limited] experience with Nextera...

In our [somewhat limited] experience with Nextera XT, we have also had some problems with the bead based normalization (in our case our case we were getting over-clustering problems). We talked with...
Forum: Illumina/Solexa 02-19-2013, 03:47 PM
Replies: 13
Views: 10,197
Posted By MicroBio
Hi oolong. This might be a little late and you...

Hi oolong. This might be a little late and you might have already decided, but I'll chime in anyways. I would think that, if you wanted to have more paired end sequences that overlap in the middle,...
Forum: Illumina/Solexa 02-09-2013, 10:34 AM
Replies: 13
Views: 10,197
Posted By MicroBio
Hi oolong. We always do BioAnalyzer on the CAN...

Hi oolong. We always do BioAnalyzer on the CAN samples (not the PAL) right after the PCR cleanup step. We do this because after library normalization the pool is ssDNA which will not work well on...
Forum: Illumina/Solexa 12-19-2012, 11:27 PM
Replies: 13
Views: 10,197
Posted By MicroBio
Thanks for the help everybody. Bumping the...

Thanks for the help everybody. Bumping the number of PCR cycles to 15 from 12 worked great. We have not sequenced the libraries yet, but right now they are looking preliminarily good for samples...
Forum: Illumina/Solexa 12-08-2012, 11:02 AM
Replies: 13
Views: 10,197
Posted By MicroBio
Question Using Lower Input DNA Concentration for Nextera XT

Hi all,

I have VERY low amounts of viral DNA which I would like to sequence using the MiSeq platform. The DNA concentrations are all below the 0.2 ng/uL recommended by Illumina (they suggest...
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