GRAND-SLAM analysis of mESCs treated with 4sU for 24h from Herzog et al., Nature Methods 2017 (https://doi.org/10.1038/nmeth.4435)

This is the processed SLAM-seq data from the 24h 4sU data set published in Herzog et al., Nature Methods  2017 (https://doi.org/10.1038/nmeth.4435). 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 sars.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 -double -reads slam_ameres_24h.cit -genomic m.ens90  -prefix grandslam_t15/24h -plot -progress

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 ameres_24h.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