GRAND-SLAM analysis of increasing 4sU concentration SLAM-seq datasets for grandRescue

These are processed datasets of 3 cell lines (U20S, HFF-TerT, HCT116) labeled for 1 hour with 4sU concentrations of 100µM, 200µM, 400µM and 800µM for the purpose of investigating 4sU-induced toxicity, mapping impairment and the potential of grandRescue to alleviate these effects.

The zip files contain 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 *.tsv.gz files are the GRAND-SLAM output tables.

To generate the GRAND-SLAM output yourself, first prepare the mouse & human genomes. Then run the following command with the respective cit-files, prefixes (*.cit) and genomes (h.ens90):

gedi -e Slam -trim5p 15 -reads *.cit -genomic h.ens90 -prefix grandslam_t15/* -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 human genome and their rRNA sequence
    Run: gedi -e Pipeline -r parallel -j *.json rnaseq_mapping.sh report.sh grandslam.sh

Software versions:

    gedi toolkit 1.0.5
    GRAND-SLAM 2.0.7
    STAR version 2.7.10b