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Bioinformatics
Tissue Sectioning
Assay Protocols and Recommendations
cDNA Amplification
Adjustments for different tissues
General
Library Preparation
Bioinformatics
Pre-processing
Secondary Analysis
Primary Analysis
Hardware/Software
Sequencing
General
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Help for the Curious
Bioinformatics
Tissue Sectioning
Assay Protocols and Recommendations
cDNA Amplification
Adjustments for different tissues
General
Library Preparation
Bioinformatics
Pre-processing
Secondary Analysis
Primary Analysis
Hardware/Software
Sequencing
General
Bioinformatics
Pre-processing
What method of clustering do we use for the UMAP?
How do you get untrimmed reads from the sequencer?
Do you have any guidance on trimming FASTQ files to 2 x 50?
Secondary Analysis
What is the conversion of coordinate system to um?
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?
How do I recalculate "median reads/UMI" after filtering out beads not covered by tissue?
How do I filter out the background in the sample?
Where can I find the bam file where reads are associated with bead barcodes and/or molecular barcodes?
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Primary Analysis
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?
What do I do if the FORMATCONVERT step fails with the following error?
CURIOSEEKER_GEN_GENE_BARCODE_UMI_DB step failed with the following error. How do I resolve it?
Hardware/Software
What are the minimum system requirements for local installation of the Curio primary analysis pipeline?