Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasets.

ABSTRACT:

Background

Single-cell RNA sequencing (scRNA-seq) has quickly become one of the most dominant techniques in modern transcriptome assessment. In particular, 10X Genomics' Chromium system, with its high throughput approach, turn key and thorough user guide made this cutting-edge technique accessible to many laboratories using diverse animal models. However, standard pre-processing, including the alignment and cell filtering pipelines might not be ideal for every organism or tissue. Here we applied an alternative strategy, based on the pseudoaligner kallisto, on twenty-two publicly available single cell sequencing datasets from a wide range of tissues of eight organisms and compared the results with the standard 10X Genomics' Cell Ranger pipeline.

Results

In most of the tested

SUBMITTER: Shainer I 

PROVIDER: S-EPMC8439043 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature