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

Some cores or commercial sequencing companies only run bigger cycle kits (2 x 150, 2 x 200, etc.). We only require 2 x 50. If you need to trim your reads, this is how you do it. General guidance for read length for informatics is as follows: a. MINIMUM of 50bp for both READ1 and READ2b. All READ1 must be the same lengthc. No adaptor trimming has been performed on READ1d. READ2 can be variable [...]

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

These are the minimum system requirements needed to install the primary analysis pipeline on your local HPC For Single-server workstation: 256G memory64 [...]

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

In certain cases, your tissue may not cover the whole tile and there will therefore be beads with background levels of signal that will affect and lower the value of "median reads/UMI". 1. To recalculate this, you will need to first filter out the beads not covered by tissue 2. Then to recalculate the "median reads/UMI": median reads/UMI = a/b where a = median number of reads per bead b = median [...]

How do I filter out the background in the sample?

Please see official documentation here: https://cdn.livehelpnow.net/clients/36168/kb/cb-000647-kb-c_may2024_suggestedworkflowforremovingofftissuesignalsfromcurioseekerdata_771971ae-b90a-4e92-96ef-644fe2dc2be7.pdf" data-file="6524a8f0-97ea-47a9-8e59-d17d751c6d2d" data-name="cb-000647-kb-c_may2024_suggestedworkflowforremovingofftissuesignalsfromcurioseekerdata Suggested workflow for removing [...]

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

Sometimes, tissue with low RNA quality or very low cellular density can cause situations where the cDNA tapestation profile is normal, but the library trace shows evidence of very long PCR-bubble products on the trace (see below). [...]