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Forum: Sample Prep / Library Generation 05-30-2018, 06:36 AM
Replies: 1
Views: 448
Posted By cement_head
Best Robotics Platform for Soil/Fecal Extraction

Anyone use a robotics platform for gDNA extraction from fecal and/or soil? If so, which robotics platform, and which kit(s)?

Thanks
Forum: Sample Prep / Library Generation 05-30-2018, 05:54 AM
Replies: 1
Views: 480
Posted By cement_head
After digging around on the web last night; the...

After digging around on the web last night; the answer seems to be "yes, treat them as per low-diversity libraries"...
Forum: Sample Prep / Library Generation 05-29-2018, 12:22 PM
Replies: 1
Views: 480
Posted By cement_head
Question RAD-Seq Library Loading Concentration?

Hello,

Would I be correct in assuming that RAD-Seq libraries should be treated as if they were low-diversity amplicon libraries (i.e. 16S rDNA/microbiome) for the purposes of loading? In other...
Forum: Illumina/Solexa 05-24-2018, 12:14 PM
Replies: 28
Views: 14,114
Posted By cement_head
For RAD-Seq libraries, to be sequenced on...

For RAD-Seq libraries, to be sequenced on Illumina MiSeq, what concentration do people typically use? Something akin to 16S metagenomics sequencing? I.E. 4.0 pM with a 10% spike-in of PhiX control?
Forum: Sample Prep / Library Generation 05-21-2018, 10:38 AM
Replies: 4
Views: 763
Posted By cement_head
Yeah, we came to the same conclusion. We tried...

Yeah, we came to the same conclusion. We tried the new Promega ProNex beads and they worked very well, and they are very, very fast at separating. Thanks.
Forum: Sample Prep / Library Generation 05-16-2018, 10:24 AM
Replies: 4
Views: 763
Posted By cement_head
What would be the disadvantage of using a...

What would be the disadvantage of using a spin-column purification, or alternate bead based purification? (i.e. AMPureXP or ProNex)?
Forum: Oxford Nanopore 05-10-2018, 06:58 AM
Replies: 15
Views: 4,694
Posted By cement_head
Okay, so the issue is NOT the minION, nor the...

Okay, so the issue is NOT the minION, nor the minKNOW software, the issue is your machine.

Do other USB thumbdrives work?

One thing to check is at BOOT, select the BIOS menu (F2, or F7 or F12...
Forum: Oxford Nanopore 05-10-2018, 06:47 AM
Replies: 15
Views: 4,694
Posted By cement_head
For some reason I can't link a image from FLICKR...

For some reason I can't link a image from FLICKR to the forum.

Basically it should show up as:

$ lsusb
Bus 002 Device 001: ID 2a1d:001 <there will be no description>
Forum: Oxford Nanopore 05-10-2018, 04:42 AM
Replies: 15
Views: 4,694
Posted By cement_head
You have to reboot after installation. If...

You have to reboot after installation.

If you've done that, without starting the MinKnow software, does your computer (OS) see the sequencer?

Open a terminal and type lsusb and see if it's...
Forum: Illumina/Solexa 05-02-2018, 08:47 AM
Replies: 14
Views: 6,080
Posted By cement_head
Question I fail to understand why people add back HCl at...

I fail to understand why people add back HCl at the end (I understand neutralising the NaOH, and bringing the pH back to "normal"), but shouldn't this be accomplished largely by the dilution of the...
Forum: Illumina/Solexa 12-16-2017, 04:27 AM
Replies: 2
Views: 740
Posted By cement_head
Question MiSeq Sequencing Short Amplicons

Hello,

If I am sequencing a heterogeneous mixture of amplicons using a MiSeq (2x250bp) to ensure overlap, and there are some short amplicons (i.e. ~ 150 bp), what happens to the run? Will the...
Forum: Bioinformatics 11-22-2017, 11:45 AM
Replies: 3
Views: 905
Posted By cement_head
Post-demultiplex adaptor removal?

If one has demultiplexed dual index reads on a MiSeq AND included "adaptor removal" as part of the demultiplexing (on instrument), should one also run the FASTQ files through an adaptor removal...
Forum: Illumina/Solexa 10-30-2017, 11:11 AM
Replies: 18
Views: 4,946
Posted By cement_head
For CLC Genomics Workbench: ...

For CLC Genomics Workbench:

https://www.qiagenbioinformatics.com/plugins/molecular-indexing
Forum: Bioinformatics 10-30-2017, 07:41 AM
Replies: 12
Views: 4,931
Posted By cement_head
If you are using CLC Genomics Workbench: ...

If you are using CLC Genomics Workbench:

https://www.qiagenbioinformatics.com/plugins/molecular-indexing
Forum: Sample Prep / Library Generation 08-25-2017, 10:39 AM
Replies: 1
Views: 664
Posted By cement_head
No, it means that Illumina no longer "SELLS"...

No, it means that Illumina no longer "SELLS" these adaptors...
Forum: Sample Prep / Library Generation 08-25-2017, 07:08 AM
Replies: 1
Views: 664
Posted By cement_head
Question PE Adaptors

In the lastest Illumina Sequence Letter, the Paired End DNA Oligonucleotides are now listed as "Obsolete". Does that mean/imply that they will no longer work on HiSeq2500 (and MiSeq) flow cells?
...
Forum: Bioinformatics 08-07-2017, 07:29 AM
Replies: 3
Views: 677
Posted By cement_head
No, there are in ONE file, PE reads, RAW FASTQ.

No, there are in ONE file, PE reads, RAW FASTQ.
Forum: Bioinformatics 08-07-2017, 05:26 AM
Replies: 3
Views: 677
Posted By cement_head
Exclamation How to "chop" a large FASTQ PE file in half?

Hello,

I hesitate to use the following terms: "split", "partition", "trim" - because they all have special connotations.

What I'd like to do is to take a large FASTQ file of PE reads and...
Forum: Illumina/Solexa 07-26-2017, 12:55 PM
Replies: 113
Views: 24,195
Posted By cement_head
Talking This whole problem is starting to make more and...

This whole problem is starting to make more and more sense to me now. Just enough sloppiness at each step probably contributes to a perfect storm of IH (Index Hopping). And given that the...
Forum: Illumina/Solexa 07-26-2017, 12:49 PM
Replies: 113
Views: 24,195
Posted By cement_head
Okay, this is interesting and jives with their...

Okay, this is interesting and jives with their basic premise. This is also contradictory to their NEXTERA i5/i7 design wherein Index codes are re-used multiple times.
Forum: Bioinformatics 07-26-2017, 09:28 AM
Replies: 33
Views: 9,910
Posted By cement_head
Hi, This is my lack of PERL shining...

Hi,

This is my lack of PERL shining through, but is there a way to get a two output files, one with the "good" reads and one with the "bad" reads?

Thanks,
Andor
Forum: Illumina/Solexa 07-20-2017, 09:46 AM
Replies: 113
Views: 24,195
Posted By cement_head
The video wasn't overly helpful, but if I...

The video wasn't overly helpful, but if I understand the patent description, they're saying that they've essentially hyper optimised the bridge amplification such that once a single seed molecule...
Forum: Illumina/Solexa 07-18-2017, 11:24 AM
Replies: 113
Views: 24,195
Posted By cement_head
Still don't understand the ExAMP chemistry, and...

Still don't understand the ExAMP chemistry, and unless I missed something, this white paper doesn't explain it. Is it that it is proprietary and largely unknown? Would you happen to have a link to...
Forum: Illumina/Solexa 07-18-2017, 07:23 AM
Replies: 113
Views: 24,195
Posted By cement_head
Does INDEX swapping (hopping) occur because this...

Does INDEX swapping (hopping) occur because this (release and re-annealing) is the method for generating clusters within each nanocell, and the swapping is as the result of the DNA fragments (library...
Forum: Illumina/Solexa 07-14-2017, 08:30 AM
Replies: 113
Views: 24,195
Posted By cement_head
What is PPM?

What is PPM?
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