inst/www/helpfiles/datamatrix_input.md

In ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Input Data

ChromSCape allows user to input a variety of different format. Depending on the output of the data-engineering/pre-processing pipeline used, the signal can be already summarized into features :

• Count matrix: features x cells tab-separated matrix. Features as rownames and cells as column names
• Peak-Index-Barcode -3 files :
  • '*_barcode.txt' : 1-column file of cell-barcode names
  • '*_peaks.bed': BED file of feature genomic location
  • '_indexes.txt': 3 column space-separated file containing row index, column index and value of non-zeroes entries in the sparse matrix

Or the signal can be stored directly in raw format (single-cell BAM,single-cell BED/BED.gz) containing genomic location of deduplicated reads for one cell.

Anyhow the format, ChromSCape needs signal to be summarized into features. If inputing raw signal (scBAM or scBED), the application lets user summarize signal of each cells into various features:

• Genomic features (extended region around TSS of genes, enhancers)
• Peaks called on bulk or single-cell signal (BED file must be provided by the user)
• Genomic bins (windows of constant length, e.g. 100kbp, 50kbp, 5kbp...)

Important note 1: For Peak-Index-Barcode, scBAM and scBED format, the user must precise the number of samples contained in the data.

Important note 2: For Peak-Index-Barcode, scBAM and scBED format, the user must place all the files in one folder and select the folder containing the files, not directly the files.

ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.