Kurmangaliyev et al., 2019 - Modular transcriptional programs separately define axon and dendrite connectivity

Some links related to the case study:

• Paper: https://elifesciences.org/articles/50822
• GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126139

Analysis of 10x Genomics Samples

BBKNN and SCENIC

The following command was used to generate the config:

nextflow pull vib-singlecell-nf/vsn-pipelines
nextflow config vib-singlecell-nf/vsn-pipelines \
    -profile sra,cellranger,pcacv,bbknn,dm6,scenic,scenic_use_cistarget_motifs,scenic_use_cistarget_tracks,singularity \
  > nextflow.config

The generated config is available at the vsn-pipelines-examples GitHub repository: kurmangaliyevyz_2019/10x_bbknn_scenic.config. You should provide the lines commented with “TO EDIT” with the correct information.

To start the pipeline, run the following command:

nextflow \
    -C nextflow.config \
    run vib-singlecell-nf/vsn-pipelines \
        -entry sra_cellranger_bbknn_scenic

The resulting loom file is available at kurmangaliyevyz_2019_bbknn_scenic.loom, and is ready to be explored in SCope.

Harmony and SCENIC (append mode)

nextflow config \
    vib-singlecell-nf/vsn-pipelines \
    -profile tenx,pcacv,harmony,scenic_append_only,singularity \
    > nextflow.config

The generated config is available at the vsn-pipelines GitHub repository: kurmangaliyevyz_2019/10x_harmony_scenic_append_only.config. You should update The lines commented with “TO EDIT” with the correct information.

To start the pipeline, run the following command:

nextflow \
    -C nextflow.config \
    run vib-singlecell-nf/vsn-pipelines \
        -entry harmony_scenic -resume

The resulting loom file is available at kurmangaliyevyz_2019/harmony_scenic_append_only and is ready to be explored in SCope.