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Forum: Pacific Biosciences 10-06-2019, 06:15 AM
Replies: 17
Views: 7,240
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: 3
Views: 400
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: 3
Views: 400
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: 2,024
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: 7,240
Posted By cement_head
Did anyone figure this out?

Did anyone figure this out?
Forum: Oxford Nanopore 05-09-2019, 02:53 AM
Replies: 5
Views: 2,935
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: 566
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, 07:25 AM
Replies: 1
Views: 2,618
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, 06:37 AM
Replies: 18
Views: 6,610
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, 03:59 AM
Replies: 4
Views: 1,161
Posted By cement_head
Okay, cool...

Okay, cool...
Forum: Sample Prep / Library Generation 04-08-2019, 09:27 AM
Replies: 4
Views: 1,161
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, 05:18 AM
Replies: 4
Views: 722
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, 05:38 PM
Replies: 4
Views: 722
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, 06:07 AM
Replies: 3
Views: 699
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, 10:44 AM
Replies: 3
Views: 699
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, 11:45 AM
Replies: 5
Views: 1,366
Posted By cement_head
We average about 50 a year...

We average about 50 a year...
Forum: Illumina/Solexa 03-08-2019, 07:05 AM
Replies: 5
Views: 1,366
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, 06:08 PM
Replies: 3
Views: 592
Posted By cement_head
Did you ask the sequencing centre how they...

Did you ask the sequencing centre how they typically demultiplex?
Forum: Illumina/Solexa 03-06-2019, 06:01 PM
Replies: 5
Views: 1,366
Posted By cement_head
MiSeq Service Contract (Bronze VS Silver)

With the "advent" of Illumina's new precious metals tiered service contracts (SCs), the bronze level seems like it doesn't cover much, not equivalent to the old "Basic" level (repairs, remote...
Forum: Bioinformatics 01-22-2019, 03:42 AM
Replies: 4
Views: 1,932
Posted By cement_head
I'm very interested in GPU-BLAST, which according...

I'm very interested in GPU-BLAST, which according to the OSC (Ohio Supercomputing Center) is at least four fold faster than CPU based BLASTing. That alone would help speed up our transcriptome...
Forum: Bioinformatics 01-22-2019, 03:17 AM
Replies: 2
Views: 1,327
Posted By cement_head
Reviving an old thread. With the advent of the...

Reviving an old thread. With the advent of the RTX nVIDIA GPU units, and the considerable efforts of nVIDIA to get people into GPU computing; we're very seriously considering buying a workstation...
Forum: Illumina/Solexa 01-03-2019, 06:07 AM
Replies: 7
Views: 1,608
Posted By cement_head
Smile Yep, you are correct - almost always USER ERROR...

Yep, you are correct - almost always USER ERROR is what we fight (constantly).
Forum: 454 Pyrosequencing 12-19-2018, 03:20 PM
Replies: 3
Views: 2,132
Posted By cement_head
Thanks - so for these specific applications, it's...

Thanks - so for these specific applications, it's still here.
Forum: 454 Pyrosequencing 12-18-2018, 07:10 AM
Replies: 3
Views: 2,132
Posted By cement_head
Qiagen "PyroSequencing"

Really dumb question, but did Qiagen revive pyrosequencing when I wasn't looking?

https://www.qiagen.com/us/resources/technologies/pyrosequencing-resource-center/technology-overview/?akamai-feo=off
Forum: Illumina/Solexa 11-29-2018, 03:07 AM
Replies: 7
Views: 1,608
Posted By cement_head
Okay, that works in a "closed" facility. What...

Okay, that works in a "closed" facility. What happens if we have an "open" facility and any user can insert a USB drive? Do I just cross my fingers?

I guess I'd like to know how to prevent usb...
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