• 109
• 0

We do not have internet access on our Linux server. When executing Seeker v3.0 pipeline with Singularity, the pipeline is unable to download containers for subread, SAMtools, and STAR. This usually results in NextFlow throwing a “Join mismatch” type error. How do I solve this?

• 66
• 0

Is the Seeker Primary Analysis Pipeline compatible with MGI/BGI sequencers?

• 91
• 0

How do I trim my FASTQ pairs to be at least 50 bp?

• 56
• 0

How do I get untrimmed reads from the sequencer?

• 78
• 0

What are the format requirements for the input FASTQ pairs?

• 77
• 0

In Read 2, are there any negatives to incorporating reads beyond the minimum 50 bp, besides needing more computing time (i.e., taking an 'as much as possible' approach)?

• 64
• 0

What versions of packages are used in the latest Seeker Primary Analysis Pipeline?

• 87
• 0

What is the structure of read 1 and read 2 in the Seeker data?

• 71
• 0

What is the unit of the spatial coordinates from the Seeker Primary Analysis Pipeline? How do I convert them to µm?

• 231
• 0

Is Curio Seeker compatible with Element Biosciences Aviti Sequencer?

• 213
• 0

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

• 333
• 0

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

• 248
• 0

What are the PhiX recommendations for the NovaSeq X Plus?

• 170
• 0

How deep should I sequence Curio Seeker libraries?

• 198
• 0

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

• 170
• 0

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

• 175
• 0

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

• 234
• 0

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