Help for the Curious

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Help for the Curious

Curio Seeker

Curio Seeker

General

What is the Curio Seeker kit?

How long does the Curio Seeker workflow take?

What is the spatial resolution of the Curio Seeker tile?

How large is the Curio Seeker tile?

Does Curio Seeker require any specialized hardware or instrumentation?

What kind of tissue and sample types can I use with the Curio Seeker kit?

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Tissue Sectioning

How do I harvest and preserve fresh frozen tissue for sectioning?

How do we use the CryoCube?

How thick should my tissue sections be for the Curio Seeker tile?

Is the use of the CryoCube essential? What if it is not used?

Assay Protocols and Recommendations

What modifications do I need to make for running Curio Seeker on plant tissue?

Do I need to make any adjustments for running Human Heart tissue?

If I have low cDNA concentration, how do I re-amplify it?

Do you need to optimize the permeabilization step for Curio Seeker?

What is difference between the Dual Indexing primer kit V1 and V2?

What if my library has indications of PCR-bubble formation?

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Bioinformatics

How do I filter out the background in the sample?

How do I recalculate "median reads/UMI" after filtering out beads not covered by tissue?

What are the minimum system requirements for local installation of the Curio primary analysis pipeline?

Do you have any guidance on trimming FASTQ files to 2 x 50?

What is the conversion of coordinate system to um?

What method of clustering do we use for the UMAP?

How do you get untrimmed reads from the sequencer?

If I have multiple regions or tissues of interest on a tile, how do I select only the beads for the region I am interested in?

CURIOSEEKER_GEN_GENE_BARCODE_UMI_DB step failed with the following error. How do I resolve it?

What do I do if the FORMATCONVERT step fails with the following error?

How do I fix the following error message? Remote resource not found: https://api.github.com/repos/nextflow-io/commercial_seeker/contents/main.nf

What do I do if the pipeline says it cannot find my STAR reference when it clearly exists?

Where can I find the bam file where reads are associated with bead barcodes and/or molecular barcodes?

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Sequencing

For the Dual Indexing Primer kit, what orientation are the sequences listed in the User Guide table?

How deep should I sequence Curio Seeker libraries?

What are the PhiX recommendations for the NovaSeq X Plus?

How much PhiX should I spike in to my library before sequencing?

What is the recommended number reads when your sample tissue does not cover the entire Tile area?

Is Curio Seeker compatible with Element Biosciences Aviti Sequencer?

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