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Forum: Illumina/Solexa 04-24-2020, 11:48 AM
Replies: 25
Views: 9,082
Posted By cement_head
Still have absolutely no idea how to do this.

Still have absolutely no idea how to do this.
Forum: Illumina/Solexa 04-23-2020, 08:46 AM
Replies: 9
Views: 974
Posted By cement_head
I'd have to agree with GenoMax; super-important...

I'd have to agree with GenoMax; super-important to have a consultation with the sequencing center about the library composition and ask them what they recommend. You probably should have had 10%...
Forum: Illumina/Solexa 04-23-2020, 08:32 AM
Replies: 1
Views: 661
Posted By cement_head
Bad NaOH... Made fresh & reloaded - now...

Bad NaOH...

Made fresh & reloaded - now working.
Forum: Illumina/Solexa 04-18-2020, 07:31 AM
Replies: 1
Views: 661
Posted By cement_head
MiSeq run failed; low clustering, but good QC

Have a strange situation, our latest MiSeq run failed for 16S - from a protocol (EMP @ ArgonneNatLabs) that we use all the time.

The clustering was unusually low (180 vs the expected 800) and we...
Forum: Sample Prep / Library Generation 04-01-2020, 02:09 PM
Replies: 11
Views: 1,745
Posted By cement_head
We do a lot of environmental (soil, lake-water)...

We do a lot of environmental (soil, lake-water) and we do sometimes get off-target bands, but we don't bother cleaning-up, just pool, reduce volume using SpeedVac, KAPA and run them on the MiSeq. We...
Forum: Sample Prep / Library Generation 03-31-2020, 06:40 AM
Replies: 11
Views: 1,745
Posted By cement_head
Interesting. I use one-step construction (EMP...

Interesting. I use one-step construction (EMP Protocol), but I could see how normalising the first step in a two step would be a good idea.
Forum: Sample Prep / Library Generation 03-31-2020, 05:36 AM
Replies: 3
Views: 3,465
Posted By cement_head
Hi, According to Eppendorf they have a...

Hi,

According to Eppendorf they have a protocol for this procedure: https://www.eppendorf.com/US-en/service-support/application-support/ngs-methods-for-epmotion/

Might contact them directly.
Forum: Sample Prep / Library Generation 03-31-2020, 05:11 AM
Replies: 0
Views: 582
Posted By cement_head
Post epMotion Programming Forum?

Hi,

Is there a epMotion programming exchange forum anywhere? I'd really be interested in sharing programmes/methods and approaches with other users.

TIA
Forum: Sample Prep / Library Generation 03-31-2020, 05:06 AM
Replies: 11
Views: 1,745
Posted By cement_head
SequalPrep Normalisation Kit (96) Load 25,...

SequalPrep Normalisation Kit (96)

Load 25, or 50 microL of PCR and wash away the rest...
Forum: Core Facilities 03-02-2020, 06:40 AM
Replies: 22
Views: 21,566
Posted By cement_head
I'd be very interested in how you managed to...

I'd be very interested in how you managed to define your own labware - can you post a guide and/or PM me? TIA
Forum: Core Facilities 03-02-2020, 06:25 AM
Replies: 22
Views: 21,566
Posted By cement_head
Is there a way for the end-user to manually tweak...

Is there a way for the end-user to manually tweak the labware definition files, and/or create new ones, or does on have to entirely rely on Eppendorf for those files?
Forum: Pacific Biosciences 12-04-2019, 06:56 PM
Replies: 6
Views: 3,857
Posted By cement_head
Interesting. HGAP4 Manual doesn't mention this,...

Interesting. HGAP4 Manual doesn't mention this, but the FALCON GitHub repo does - the impression that SMRTLink software gives is that it is a GUI wrapper for FALCON. I guess not. Thanks.
Forum: Pacific Biosciences 12-04-2019, 12:07 PM
Replies: 2
Views: 3,463
Posted By cement_head
Curious as to how long the HGAP4 assembler took...

Curious as to how long the HGAP4 assembler took and what were the specs on your computer/cluster?
Forum: Pacific Biosciences 11-19-2019, 04:45 AM
Replies: 6
Views: 3,857
Posted By cement_head
Well, finally got version 8 installed. It never...

Well, finally got version 8 installed. It never completes, just hangs forever. Seems like a terrible assembler.
Forum: Sample Prep / Library Generation 11-12-2019, 03:17 AM
Replies: 21
Views: 7,259
Posted By cement_head
Ha! Talk of the Devil! New kit by Qiagen... ...

Ha! Talk of the Devil!

New kit by Qiagen...
...
Forum: Sample Prep / Library Generation 11-11-2019, 06:26 PM
Replies: 21
Views: 7,259
Posted By cement_head
Interesting...micrboEXPRESS looks to be an Ambion...

Interesting...micrboEXPRESS looks to be an Ambion Kit (originally). But Ambion basically got destroyed when Thermo Fisher bought it...
Forum: Sample Prep / Library Generation 11-11-2019, 05:13 PM
Replies: 21
Views: 7,259
Posted By cement_head
Has anyone tried this kit from ZYMO? Usually...

Has anyone tried this kit from ZYMO? Usually ZYMO stuff is pretty good...

https://www.zymoresearch.com/products/zymo-seq-ribofree-universal-cdna-kit
Forum: Sample Prep / Library Generation 10-30-2019, 07:20 AM
Replies: 2
Views: 1,329
Posted By cement_head
(2x) Final Bead Clean-Up

Hello,

I have a general question regarding NGS library prep protocols; many of the protocols suggest using TWO rounds of bead clean-up at the end of the protocol. I am curious as to why TWO (2)...
Forum: Pacific Biosciences 10-06-2019, 06:15 AM
Replies: 17
Views: 10,131
Posted By cement_head
Check the GitHub for PacBio, they have a...

Check the GitHub for PacBio, they have a converter. Here's the URL: https://github.com/PacificBiosciences/bam2fastx
Forum: Pacific Biosciences 10-06-2019, 06:09 AM
Replies: 6
Views: 3,857
Posted By cement_head
Cool Well, figured it out - was a corrupted file from...

Well, figured it out - was a corrupted file from the download!

Wood Frog Genome - 6 Gbp

Got it working, but it barfs as it wants to fo a 30x coverage and from the RAW reads, it comes up a few...
Forum: Pacific Biosciences 10-03-2019, 12:54 PM
Replies: 6
Views: 3,857
Posted By cement_head
SMRT Link 7.0 - HGAP

Has anyone gotten the HGAP assembler to work? It seems that it just barfs at different places constantly. Doesn't seem to be very robust at all.

I've used CANU before, so I'm going to try to go...
Forum: Pacific Biosciences 09-29-2019, 12:47 PM
Replies: 3
Views: 3,410
Posted By cement_head
May this will help?...

May this will help? https://github.com/PacificBiosciences/bam2fastx
Forum: Pacific Biosciences 09-29-2019, 12:34 PM
Replies: 17
Views: 10,131
Posted By cement_head
Did anyone figure this out?

Did anyone figure this out?
Forum: Oxford Nanopore 05-09-2019, 02:53 AM
Replies: 6
Views: 5,406
Posted By cement_head
Okay, so you would then type in the IP of the...

Okay, so you would then type in the IP of the machine running the minKNOW instance and it would be mirrored on your (remote) machine?
Forum: Illumina/Solexa 05-05-2019, 03:18 PM
Replies: 0
Views: 770
Posted By cement_head
MiSeq transcriptome [load]

Hi,

We're doing a quick & dirty transcriptome for a low-complexity tissue using a single library on a MiSeq; time/cost are a factor. The run is a single sample RNA-Seq; V2 reagent; 2x150 PE. ...
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