Application notes
Notes
One failure per page, written from the matching tool. HTML, not a gated PDF.
Cell Ranger
Why a dot in the sample prefix hides FASTQs from Cell Ranger
Cell Ranger splits Illumina FASTQ names on a period. A dot inside the sample prefix makes --sample miss valid reads. How to see it, and how to repair the name without touching sequence.
Why Cell Ranger misses FASTQs with a dot in the sample prefix →
Cell Ranger
Why NCBI SRA _1/_2 FASTQ names need review before Cell Ranger
fastq-dump writes SRR…_1.fastq.gz. Cell Ranger wants an Illumina suffix. The mapping is usually R1/R2, but three-file dumps exist, so the planned renamer proposes a name and does not apply it until you confirm read identity.
Plate planner
Why keep samples off the edge wells of a 96-well plate
The outer 36 wells of a 96-well plate are the usual source of evaporation and position bias. The planner can reserve them, put blanks or controls there, and report it if a sample still lands on the edge.
Indexes
Why Hamming distance 1 between Illumina indexes is a failed pool
Demultiplexing needs leftover substitutions after an error. Distance 1 cannot provide that, and combinatorial dual indexes add an index-hopping failure even when the pair looks unique.