A collaborative project of UniCA’s biology institutes
A FASTQ file is a text-based format which stores both the nucleotides sequence of each read and its corresponding quality scores.
Common extensions : .fastq
A matrix of gene expression raw counts. Depending on resolution, it can be a gene x sample, gene x cell or gene x spot matrix. For single cell RNA-seq data outputs from 10X or Parse pipelines, row and column name could be in separated .tsv files, but in the same folder than the .mtx file.
Common extensions : .mtx, .tsv, .csv, .txt, .h5, .h5ad
Text file indicating spatial positions of each cell/spot
Common extensions : .tsv
Annotated data matrices are complex data classes designed to efficiently store and handle high-dimensional count matrices associated with their row/column annotations. They are particularly useful for the analysis of single-cell data, where they also centralize information on data transformations (normalization, dimension reduction, projections, etc.) that have been performed during the analysis process. Most downstream analysis functions and tools use them as input, whether in R (seurat or sce objects) or in Python (anndata object class).
Common extensions : .rds, .h5, .h5ad
beta matrix is a topics x genes matrix, indicating for each topic the expression of each overly dispersed genes
Common extensions : .rds, .txt, .xlsx
Differential analysis table are common outputs of statistical comparison of biological molecules quantified at a particular omics level.
Common extensions : .csv, .tsv, .txt, .xlsx
theta matrix is a spots barcodes x topics proportion matrix, indicating for each spot the proportion of each topic
Common extensions : .rds, .txt, .xlsx