How deep should I sequence Curio Seeker libraries?

Although we recommend 200-600 million paired-end reads for the 3x3 mm tile and 2-3 billion paired-end reads for the 10x10 mm tile, deeper sequencing may be required for more transcriptionally active tissue types. In the html output file from the Curio bioinformatics pipeline, the metric "median reads/UMI" indicates the approximate sequencing saturation. We recommend a value of 8-10 to reach [...]

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

For the following table: src="https://customerportal.curiobioscience.com/hs-fs/hubfs/image-png-Dec-15-2023-06-37-07-1761-PM.png?width=728&height=481&name=image-png-Dec-15-2023-06-37-07-1761-PM.png The orientation for the i7 indices should be entered into the spreadsheet as is. The orientation of the i5 bases should be entered as is for NovaSeq 6000 with v1.0 reagent kits, MiSeq, HiSeq [...]

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

bam, v2.0.0, bead barcodes, molecular barcodes, bam tags v2.0.0 does not generate a bam file where reads are associated with bead or molecular barcodes. However, the association can be generated by merging two of the pipeline’s intermediate output (r1-db and r2-db). The output will be a parquet file where each row is a read - read IDs and bead barcode sequences are defined for each row. Merging [...]

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

Failure mode the `NF:CURIOSEEKER:PRIMARY_READ2:STAR_ALIGN (Mouse_spleen_1M)` Process dies after three retries with the following error: src="https://customerportal.curiobioscience.com/hs-fs/hubfs/image-png-Jan-12-2024-08-51-15-5553-PM.png?width=621&height=587&name=image-png-Jan-12-2024-08-51-15-5553-PM.png [...]

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

Make sure that the commercial seeker/ http://main.nf/" target="_blank main.nf in the triggering command points to the http://main.nf/" target="_blank main.nf file within the commercial_seeker-1.0.3 folder ( commercial_seeker-1.0.3/ http://main.nf/" target="_blank main.nf [...]