RNAseq service recommendations
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4.9 years ago
mkh ▴ 60

Hi All,

I have recently started RNA-seq and ChiP-Seq assay and wanted to ask your advice as to where you guys recommend I could have them sequenced? I have the recommendation to use the Yale Facility but I have heard good things about other services, private and otherwise. What do you recommend? And which of these NGSs recommended? HiSeq2500, Hiseq4000, NovaSeq and MiSeq

Thank you,

next-gen rna-seq • 1.3k views
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Check https://allseq.com and https://genohub.com/ for comparative pricing from multiple providers. Ask your neighbors to see what they use. Consider supporting your local sequencing facility, when you can.

And what is the difference between HiSeq2500, Hiseq4000, NovaSeq and MiSeq?

All the info you need: https://www.illumina.com/systems/sequencing-platforms.html

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And what is the difference between HiSeq2500, Hiseq4000, NovaSeq and MiSeq?

Have you tried searching online to look for differences? Please show us you have invested effort in trying to answer your own questions.

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Thank you. I am sorry for my bad question. So I edited my question to following: Which of these NGSs sequencers recommended HiSeq2500, Hiseq4000, NovaSeq and MiSeq

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That is your choice, depending on funds you have available, amount of data you need/want and other ephemeral factors such as how quickly your provider can get you the data, does your institutional policy allow the data to be sequenced overseas (especially if these are human clinical samples) etc.

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4.9 years ago
maxwhjohn1988 ▴ 130

I recently had a PE cDNA library constructed and sequenced by Eurofins (they're in Germany). They were cheap, relatively fast (although not incredible on that front), and the data were very high quality. For DNA library construction and sequencing I've used Novogene [for wgs/Illumina PE, 90 samples] (based in China and now the UK too, cheap but inflexible, good data eventually but good luck getting them to admit or even understand if they've made a mistake, heard on the grapevine afterwards that they are very open to haggling over prices), GeneWiz [for wgs/Illumina, 2 samples] (based in NJ, no complaints and cheap, for a two libraries) and PMGC [for 10x Genomics, wgs/Illumina, 2 samples] (attached to the U. of Toronto, cheap, helpful, disorganised, but was at the time newly established and is now under different management, so may have improved).

Costs (and quality) will vary considerably depending on the platform you want to use, the total volume of sequencing data you need, and on whether you do library preparation yourself. Sequencing providers also seem to vary a lot in terms of how their costs scale with the number of samples or libraries you want sequenced - some get prohibitively expensive very fast, others start expensive for one sample or library but scale more acceptably as you add more samples / libraries.

The website https://genohub.com exists to connect sequencing service providers with customers based on customer requirements. I did tap them for a quote a year or so ago and they were extremely pro-active (I think their reps work on a commission basis). I ultimately went somewhere else (and regretted it!)

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