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fls-bioinformatics-core / auto_process_ngs

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.
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Explicitly disable adapter trimming when generating Fastqs for 10x Genomics Visium data #886

Closed pjbriggs closed 10 months ago

pjbriggs commented 10 months ago

The 10x_visium protocol in the Fastq generation pipeline needs to be updated to explicitly disable adapter trimming, based on the following comment in the documentation for the 10x Genomics spaceranger softare:

Do not trim adapters during demultiplexing. Leave these settings blank. Trimming adapters from reads can potentially damage the 10x barcodes and the UMIs, resulting in pipeline failure or data loss.

See https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/using/mkfastq#:~:text=spaceranger%20mkfastq%20supports%20listing%20either,pipeline%20failure%20or%20data%20loss.

pjbriggs commented 10 months ago

Turns out this has already been implemented, so nothing to do.