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Introduction Version

Scanpy Load count matrices

Typing name :  TASK.gws_scomix.ScanpyLoadData Brick :  gws_scomix

This task permit to load count matrices belonging to multiple samples and stored in different format

-This task permit to load count matrices belonging to multiple samples. In fact, these files could be generated using different tools cellranger or STAR solo (there is already a task for STAR solo). -Using this task permits also to eliminate cells predected to be doublet. It also permits to visualize the distribution of mitochondrial,ribosomal,hemoglobin genes and the number of genes with at least 1 count in a cell. -It allows also to generate a table containing the min and max values in each of these parameters. -Finally the concatenated data stored in .h5ad format will be used to perform the preprocessing and data filtring. -In term of input file format : .h5 ; .csv ; matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz or matrix.mtx, barcodes.tsv , features.tsv. -IMPORTANT : Please verify that your files are named as follow !!! * For .h5 and .csv file : samplename_what_you_want_to_put.h5 or samplename_what_you_want_to_put.csv * For matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz or matrix.mtx ,barcodes.tsv ,features.tsv : samplename_matrix.mtx.gz , samplename_features.tsv.gz , samplename_barcodes.tsv.gz or samplename_matrix.mtx , samplename_features.tsv , samplename_barcodes.tsv * samplename could be : patient1 or PATIENT1 or P2 or pat2 or PAT2 or control1 or CONTROL5 or ctr1 ect ....


count matrices folder
count matrices in different file format belonging to different individuals


This file contain raw data
Metadata associated to each cell
This table stores metadata associated with each cell such as mitochondrial content , number of counts etc
Statistical table
This file contain the min_max values in term of mitochondrial and ribosomal percentage , genes per count and total counts