GRAND-SLAM analysis of acute BANP depletion from Grand et al., Nature 2021 (https://doi.org/10.1038/s41586-021-03689-8)

This is the processed SLAM-seq data from the SLAM-seq data set published in Grand et al., Nature 2021 (https://doi.org/10.1038/s41586-021-03689-8). The zip file contains the full output from the processing pipeline (including the mapped reads, the scripts to run the pipeline and the output). The json file is required if you want to start from scratch. The file BANP.tsv.gz is the GRAND-SLAM output table.

To generate the GRAND-SLAM output yourself, first prepare the mouse (ensembl v90). Then run:

gedi -e Slam -trim5p 15 -reads BANP.cit -genomic m.ens90 -prefix grandslam_t15/BANP -plot  -D -modelall

To generate the cit file you have to modify the first lines in start.bash to match the paths on your file system, and then run it.

You can also start from scratch (i.e., the json file):

    Prepare the mouse genome (ensembl v90) and the murine rRNA sequence
    Run: gedi -e Pipeline -r parallel -j BANP.json rnaseq_mapping.sh report.sh grandslam.sh

Software versions:

    gedi toolkit 1.0.4
    GRAND-SLAM 2.0.7
    STAR version 2.5.3a