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Search: Posts Made By: cement_head
Forum: Pacific Biosciences 12-04-2019, 07:56 PM
Replies: 6
Views: 1,793
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, 01:07 PM
Replies: 2
Views: 2,447
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, 05:45 AM
Replies: 6
Views: 1,793
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, 04:17 AM
Replies: 16
Views: 4,324
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, 07:26 PM
Replies: 16
Views: 4,324
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, 06:13 PM
Replies: 16
Views: 4,324
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, 08:20 AM
Replies: 2
Views: 537
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, 07:15 AM
Replies: 17
Views: 7,898
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, 07:09 AM
Replies: 6
Views: 1,793
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, 01:54 PM
Replies: 6
Views: 1,793
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, 01:47 PM
Replies: 3
Views: 2,291
Posted By cement_head
May this will help?...

May this will help? https://github.com/PacificBiosciences/bam2fastx
Forum: Pacific Biosciences 09-29-2019, 01:34 PM
Replies: 17
Views: 7,898
Posted By cement_head
Did anyone figure this out?

Did anyone figure this out?
Forum: Oxford Nanopore 05-09-2019, 03:53 AM
Replies: 5
Views: 3,310
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, 04:18 PM
Replies: 0
Views: 616
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. ...
Forum: Illumina/Solexa 04-24-2019, 08:25 AM
Replies: 1
Views: 2,709
Posted By cement_head
Hello, I had the same question. I have...

Hello,

I had the same question. I have been using Genomic-Tips (100) on the assumption that they gave excellent results (quality & yield), but I'm questioning the yields stated in the Qiagen...
Forum: Illumina/Solexa 04-10-2019, 07:37 AM
Replies: 18
Views: 6,933
Posted By cement_head
Replacement for BiomekFX

Hello,

We currently have a BiomekFX, but it's getting to be near EOL for support/add-ons. We're wondering what people are using? I will NOT buy Perkin-Elmer; they're overpriced and...
Forum: Sample Prep / Library Generation 04-09-2019, 04:59 AM
Replies: 4
Views: 1,241
Posted By cement_head
Okay, cool...

Okay, cool...
Forum: Sample Prep / Library Generation 04-08-2019, 10:27 AM
Replies: 4
Views: 1,241
Posted By cement_head
AMPureXP beads > 18 months old?

Has anyone used AMPureXP beads older than 18 months, (assuming that they were stored properly)?
Forum: Sample Prep / Library Generation 04-03-2019, 06:18 AM
Replies: 4
Views: 825
Posted By cement_head
No, I don't want the small fragments. I want...

No, I don't want the small fragments. I want only fragments LARGER than 1000 bp.

In essence, I want to eliminate any small (unseen) fragments that may unduly influence a nanopore/ONT minION...
Forum: Sample Prep / Library Generation 04-02-2019, 06:38 PM
Replies: 4
Views: 825
Posted By cement_head
Bead removal of <1000 bp from LARGE fragments

Hi,

Trying to prep some very large fragment libraries (>50 kbp), and I've isolated the gDNA using a BluePippin, but when I use beads (Promega ProNex) to clean up, or rather, remove the small...
Forum: Illumina/Solexa 03-21-2019, 07:07 AM
Replies: 3
Views: 772
Posted By cement_head
Okay, I guess it's just that the "cost per base"...

Okay, I guess it's just that the "cost per base" is significantly higher than the 3000/4000 series; that's why we're seeing a reduction in availability. It's too bad because they don't suffer from...
Forum: Illumina/Solexa 03-20-2019, 11:44 AM
Replies: 3
Views: 772
Posted By cement_head
Is the HiSeq2500 DOA?

Is the HiSeq2500 being phased out? In other words, has it reached EOL and/or is Illumina ceasing to provide supply reagents?

Thanks,
Andor
Forum: Illumina/Solexa 03-08-2019, 12:45 PM
Replies: 5
Views: 1,508
Posted By cement_head
We average about 50 a year...

We average about 50 a year...
Forum: Illumina/Solexa 03-08-2019, 08:05 AM
Replies: 5
Views: 1,508
Posted By cement_head
YES! I remember that when we were pitched. I've...

YES! I remember that when we were pitched. I've NEVER had anything break in three years - ever, except a hard drive, which I could have easily fixed myself.

Think I might do the Bronze and just...
Forum: Illumina/Solexa 03-06-2019, 07:08 PM
Replies: 3
Views: 632
Posted By cement_head
Did you ask the sequencing centre how they...

Did you ask the sequencing centre how they typically demultiplex?
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