single_cell_toolkit
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aertslab
Tools for correcting single cell barcodes for various scATAC-seq techniques and creating fragment files and spltting BAM files per cluster.
Currently 10x multiome data (and some Cell Ranger versions) are not supported by `calculate_saturation_10x_samples.py`. There are different paths to the summary metrics file for multiome, RNA and ATAC, and these...
> cat PUMATAC_tutorial-main/PUMATAC/src/singlecelltoolkit/processes/barcode_correction.nf nextflow.enable.dsl=2 //binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/singlecelltoolkit/bin/" : "" toolParams = params.tools.singlecelltoolkit process SCTK__BARCODE_CORRECTION { container toolParams.container label 'compute_resources__sctk_barcode' input: tuple val(sampleId), val(technology), path(fastq_PE1), path(fastq_bc), path(fastq_PE2), path(bc_whitelist) output:...
I just ran into this same issue (https://github.com/aertslab/pycisTopic/pull/158) running single_cell_toolkit as part of the PUMATAC pipeline. In short, when using genomes with inconsistent string/integer chromosome names polars can incorrectly infer...
