Yes! All QuantSeq FWD and REV kits ordered after November 2016 are supplied with a code to access the free QuantSeq data analysis pipelines on the BlueBee® Genomics Platform.
The code supplied with the QuantSeq FWD Kits enables two different pipeline options:
FWD pipeline – For standard QuantSeq FWD library data (no UMIs).
FWD-UMI pipeline – only for libraries prepared with the UMI Second Strand Synthesis Module for QuantSeq FWD (Illumina, Read 1, Cat. No. 081).
analyses. Please see our Data Analysis FAQs for more information. Each code contains an equal number of pipeline analysis runs as reactions provided in the kits, i.e., you should choose either the FWD or FWD-UMI pipeline, depending on how your libraries were prepared. If you wish to run both options, additional Activation Codes will need to be purchased (Cat. No. 090). If you start the wrong pipeline for your data you can abort or stop the run before it is completed without losing your allocated runs. If the run is completed then additional runs will need to be purchased.
To analyze data from QuantSeq FWD libraries that contain UMIs (prepared with the UMI Second Strand Synthesis Module (Cat. No. 081), simply use the activation code included with your QuantSeq FWD kit and select the respective pipeline when setting up your data analysis run on BlueBee®.
QuantSeq FWD libraries prepared from blood using Globin Block (RS-GBHs or RS-GBSs, Cat. No. 070 and 071) should be analyzed using the standard FWD pipeline for data analysis; unless UMIs are also included and then the FWD-UMI pipeline should be selected.
NOTE! Do not run the "FWD-UMI" pipelines for QuantSeq FWD (standard) libraries that do not contain UMIs. This will incorrectly collapse reads and result in incorrect read count data. Use only the FWD pipelines for standard QuantSeq FWD libraries!
Be sure to only select the "FWD-UMI" pipelines for UMI-containing libraries, otherwise duplicate reads will not be collapsed.
ATTENTION: Data Analysis access is only free using the provided code, for fastq input files up to 1.5 GB in size. Larger fastq file sizes can only be processed using activation codes for large file sizes, which can be purchased additionally (Cat. No. 093 for FWD, or Cat. No. 094 for REV library types, respectively). Do not use activation codes provided with the QuantSeq REV Kit (Cat. No. 016) for analysis of FWD libraries.
Analysis pipelines for QuantSeq (FWD, FWD-UMI, and REV) are currently available for the following species:
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Common name (if available)
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Species
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African Oil Palm
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Elaeis guineensis
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Arabidopsis
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Arabidopsis halleri
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Arabidopsis Thale cress
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Arabidopsis thaliana
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Baker's Yeast
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Saccharomyces cerevisiae
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Barley
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Hordeum vulgare
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Bartonella
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Bartonella henselae
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Brain-Eating Amoeba
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Naegleria fowleri
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Chicken
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Gallus gallus
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CHO-K1 Cell Line
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Cricetulus griseus
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Common Yellow Monkeyflower
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Mimulus guttatus
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COVID19
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SARS-CoV-2
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Cow
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Bos taurus
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Cacao Tree
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Theobroma cacao criollo
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Dog
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Canis lupus familiaris
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Drummond's Rockcress
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Boechera stricta
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Ferret
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Mustela putorius furo
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Fruit Fly
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Drosophila melanogaster
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Fungus
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Fusarium oxysporum
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Fungus
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Yarrowia lipolytica
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Goat
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Capra hircus
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Human
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Homo sapiens
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Maize/Corn
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Zea mays
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Melon Fly
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Bactrocera cucurbitae
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Mouse
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Mus musculus
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Nematode Roundworm
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Caenorhabditis elegans
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Painted Turtle
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Chrysemys picta bellii
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Pig
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Sus scrofa
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Potato
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Solanum tuberosum
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Pseudomonas
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Pseudomonas aeruginosa PA103
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Purple False Brome
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Brachypodium distachyon
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Rabbit
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Oryctolagus cuniculus
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Rat
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Rattus norvegicus
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Rice
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Oryza sativa
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Salmon
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Salmon salar
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Sorghum
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Sorghum bicolor
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Sponge
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Amphimedon queenslandica
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Starlet Sea Anemone
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Nematostella vectensis
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Tomato
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Solanum lycopersicum
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Water flea
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Daphnia pulex
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Western Balsam Poplar Tree
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Populus trichocarpa
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Yeast
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Candida albicans, Candida auris, Candida parapsilosis
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Yeast
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Kluyveromyces lactis
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Zebrafish
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Danio rerio
New species can be added upon request for an additional fee. Please contact support@lexogen.com if your species of interest is not listed, and for pricing information. a 96 reaction kit includes 96 data analysis runs.
The list of reference annotations available for the pipelines can be found here: What species are available for my data analysis?
NOTE: Our QuantSeq-Pool Kit does not come with free access to data analysis pipelines. Please check this online FAQ How do I analyze my QuantSeq-Pool data?
File Sizes
The FASTQ input file size limit for free data analysis runs is 1.5 GB. Larger FASTQ file sizes may require additional quotas which can be purchased separately at sales@lexogen.com (Cat. No. 211 and 212 for QuantSeq FWD; Cat. No. 213 and 214 for QuantSeq REV). Alternatively, you can also try to compress your FASTQ files. For more information on how to achieve this, please this online FAQ My FASTQ files are bigger than 1.5GB what should I do?