yaximik, you can provide custom sequencing primers for single lanes of a HiSeq 2000. We do it all the time for our nextRAD markers. The University of Oregon sequencing facility is used to custom jobs, so check with them (http://htseq.uoregon.edu/).
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
Originally posted by SNPsaurus View Postyaximik, you can provide custom sequencing primers for single lanes of a HiSeq 2000. We do it all the time for our nextRAD markers. The University of Oregon sequencing facility is used to custom jobs, so check with them (http://htseq.uoregon.edu/).
Shawn
www.allseq.com
Comment
-
Originally posted by GenoMax View PostHere is an example cost estimator you can try (without having to contact anyone): [url]https://dugsim.net/estimate_cost[/url
But the opp to get multiple quoting is interesting, thanks!
Comment
-
Originally posted by SNPsaurus View Postyaximik, you can provide custom sequencing primers for single lanes of a HiSeq 2000. We do it all the time for our nextRAD markers. The University of Oregon sequencing facility is used to custom jobs, so check with them (http://htseq.uoregon.edu/).
Comment
-
Originally posted by AllSeq View PostSNPsaurus is right - you can't share lanes with anyone, but you don't necessarily need to buy an entire flow cell (just depends on how much coverage you want). We'd be happy to help you find the right provider - just let me know.
Shawn
www.allseq.com
Comment
-
Originally posted by GenoMax View PostHere is an example cost estimator you can try (without having to contact anyone): https://dugsim.net/estimate_cost
Following sites give you access to multiple providers for quotes:
AllSeq: http://www.allseq.com/
Genohub: https://genohub.com/
Comment
-
-
Originally posted by ymc View PostDoes that mean you can put one exome and one rna on the same lane?
What I found unexpectedly in my search is that 2 weeks run on 2000/2500 seems less favorable because of the drop in the quality as reagents are sitting on the machine too long. Although it can produce more output (up to 300 GB?), how much data is lost after filtering bad reads? One day run on 2500 can produce up to 60GB or 2x30GB. It is a bit more expensive per GB, but the quality got to be higher and less data are lost after filtering low quality reads. How drastic is the difference?
With an average $3.5K per lane the slow mode will produce 30x6=180GB in 2 weeks for about $21K. The same 30x6=180GB can be produced by 3 fast mode two lane runs for about 3x$6K=$18K in less than a week, but with much better quality. So how the amounts of data are compared after quality filtering?
Comment
-
High-output flowcells for the Hiseq are prepared on an ancillary piece of equipment known as a cBot.
The cBot pulls reagents through each lane separately, including libraries and their associated sequencing primers, and thus it is quite possible to have multiple different projects on the same flowcell, with each lane theoretically able to have its own sequencing primer or mix of primers. If you couldn't have multiple samples across the lanes of a flowcell, the whole operation would not be eve close to cost effective.
Where you would run into trouble is the turn-around chemistry, which happens onboard the Hiseq and does have all lanes pulling out of the same read2 primer mix. One could, again theoretically, spike in another primer in this tube and you might be able to get a custom read 2. Or you could just replace this tube completely with a tube of your own primer mix, assuming all 8 lanes require the same primer(s).
The overall drop in quality over a 10 day run is negligible for a library of good quality and a lab that knows how to run their sequencer. While it is true that the Rapid mode has less of a Q score drop over the length of its run (generally speaking, again assuming proper libraries and usage) the overall drop in quality is more of a technicality than an actual data analysis issue.
If you're paying more than $3k per lane for high-output on the Hiseq I think you're being overcharged. I've attached a price breakdown showing what I charge for academic users and the associated cost per M reads and Gbp.
My average high-output mode gives 38x8=304Gbp over 10 days for a little less than $19k. The same amount of data from a Rapid (with the same read lengths) would take 5 runs for a little more than $20k
You will always pay a penalty for Rapid mode runs.
Comment
-
Originally posted by GW_OK View PostHigh-output flowcells for the Hiseq are prepared on an ancillary piece of equipment known as a cBot.
The cBot pulls reagents through each lane separately, including libraries and their associated sequencing primers, and thus it is quite possible to have multiple different projects on the same flowcell, with each lane theoretically able to have its own sequencing primer or mix of primers. If you couldn't have multiple samples across the lanes of a flowcell, the whole operation would not be eve close to cost effective.
Where you would run into trouble is the turn-around chemistry, which happens onboard the Hiseq and does have all lanes pulling out of the same read2 primer mix. One could, again theoretically, spike in another primer in this tube and you might be able to get a custom read 2. Or you could just replace this tube completely with a tube of your own primer mix, assuming all 8 lanes require the same primer(s).
The overall drop in quality over a 10 day run is negligible for a library of good quality and a lab that knows how to run their sequencer. While it is true that the Rapid mode has less of a Q score drop over the length of its run (generally speaking, again assuming proper libraries and usage) the overall drop in quality is more of a technicality than an actual data analysis issue.
If you're paying more than $3k per lane for high-output on the Hiseq I think you're being overcharged. I've attached a price breakdown showing what I charge for academic users and the associated cost per M reads and Gbp.
My average high-output mode gives 38x8=304Gbp over 10 days for a little less than $19k. The same amount of data from a Rapid (with the same read lengths) would take 5 runs for a little more than $20k
You will always pay a penalty for Rapid mode runs.
Comment
-
-
-
Originally posted by ymc View PostIf the cost of Rapid PE100 is $4,099, how can Duke offer $4,453???
Originally posted by ymc View PostOh I see. Your price is actually the academic price. So you are even cheaper than Duke.
Do you guys take non-academic projects?
Originally posted by yaximik View PostWow, if you can do 60 GB for about $4К - I am your customer!
Originally posted by GenoMax View Post@GW_OK Hope you have space capacity available since everyone is going to want to send sequencing your way
Are those prices meant *only* for in-house academic customers? Are they per lane or per flowcell prices?
Originally posted by GenoMax View PostI doubt GW_OK is guaranteeing that volume of data for the price. If your libraries are good quality then that number is a guide to output you can expect.
If you're interested in having some work done my contact info is on my (currently outdated) core website:
Comment
Latest Articles
Collapse
-
by seqadmin
The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...-
Channel: Articles
11-06-2024, 07:24 PM -
-
by seqadmin
Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...-
Channel: Articles
10-18-2024, 07:11 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 11-08-2024, 11:09 AM
|
0 responses
210 views
0 likes
|
Last Post
by seqadmin
11-08-2024, 11:09 AM
|
||
Started by seqadmin, 11-08-2024, 06:13 AM
|
0 responses
154 views
0 likes
|
Last Post
by seqadmin
11-08-2024, 06:13 AM
|
||
Started by seqadmin, 11-01-2024, 06:09 AM
|
0 responses
80 views
0 likes
|
Last Post
by seqadmin
11-01-2024, 06:09 AM
|
||
New Model Aims to Explain Polygenic Diseases by Connecting Genomic Mutations and Regulatory Networks
by seqadmin
Started by seqadmin, 10-30-2024, 05:31 AM
|
0 responses
26 views
0 likes
|
Last Post
by seqadmin
10-30-2024, 05:31 AM
|
Comment