GRAND-SLAM analysis comparing SLAM- and TUC-seq datasets and SLAM-seq in fixed cells for grandRescue

These are two processed datasets comparing 4sU induced dropout in SLAM-seq versus TUC-seq and SLAM-seq in fixed cells compared to normal SLAM-seq.

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 genome. Then run the following command with the respective cit-files, prefixes (*.cit) and genome:

gedi -e Slam -trim5p 15 -reads *.cit -genomic m.ens102 -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 mouse 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