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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 Platformanalyses. Each code contains an equal number of pipeline analysis runs as reactions provided in the kits, i.e., a 96 reaction kit includes 96 data analysis runs.
The list of reference annotations available for the pipelines hosted on the BlueBee Genomics Platform can be found here: /wiki/spaces/TS/pages/78676050
NOTE: QuantSeq-Flex and QuantSeq-Pool Kits do not come with free access to data analysis pipelines on the BlueBee Genomics Platform. Please check these the respective FAQs for data analysis information for these kits:
File Sizes
The FASTQ input file size for free data analysis runs on the BlueBee Genomics Platform is 1.5 GB. Larger FASTQ file sizes can only be processed using activation codes for large file sizes, which can be purchased additionally (Cat. No. 093 211 and 112 for QuantSeq FWD, or ; Cat. No. 094 213 and 214 for QuantSeq REV library types, respectively). For additional options to collapse FASTQ files for analysis, see: My FASTQ files are bigger than 1.5 GB what should I do?.
Which Pipeline Should I Choose?
The pipelines for FWD and REV are selected automatically based on the type of kit 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®.
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).
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).
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.
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.
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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!
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For detailed information on how to use your data analysis codes from January 2023, please consult the following FAQs:
Additional information can be found in the following FAQ section: /wiki/spaces/TS/pages/377749517