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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Handling Evrogen Mint PlugOligo-1 adapter sequences #46

Closed chris-rands closed 4 years ago

chris-rands commented 5 years ago

I ran R2 of my FASTQ 10X sequencing data through FastQC and I found several over represented short sequences (up to 2% of sequences) at the start/end of reads, apparently deriving from Evrogen Mint PlugOligo-1 adapters. I'm not sure how these adapters were introduced? Will CellRanger handle them appropriately or should they be trimmed before running cellranger count? Thanks

chris-rands commented 4 years ago

According to the 10x support team, the adapter-like sequences are in fact the Template Switch Oligo (TSO). Given the relatively low levels of contamination, it is unlikely to be problematic

chris-rands commented 4 years ago

In CellRanger v4 they have actually changed the behviour-- "When analyzing 3’ Gene Expression data, Cell Ranger 4.0 trims the template switch oligo (TSO) sequence from the 5’ end of Read-2 and the poly-A sequence from the 3’ end before aligning reads to the reference transcriptome. This behavior is different from Cell Ranger 3.1, which does not perform any trimming." https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/release-notes