GRAND-SLAM analysis of NXF1 knockout cells from Zuckerman et al., Mol Cell 2020 (https://doi.org/10.1016/j.molcel.2020.05.013)

This is the processed SLAM-seq data from Zuckerman et al., Mol Cell 2020 (https://doi.org/10.1016/j.molcel.2020.05.013). 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 nxf1.tsv.gz is the GRAND-SLAM output table.

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

gedi -e Slam -trim5p 15 -reads nxf1.cit -genomic h.ens90 -prefix grandslam_t15/nxf1 -plot -progress

To generate the cit file you have to modify the paths in all scripts/* to match the paths on your file system, and then run star.bash.

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

1. Prepare the human genome (ensembl v90), the human rRNA sequence (U13369.1), and the Mycoplasma hominis sequence
2. Run: gedi -e Pipeline -r parallel -j nxf1.json rnaseq_mapping.sh report.sh grandslam.sh

Software versions:

• gedi toolkit 1.0.2
• GRAND-SLAM 2.0.5g
• STAR version 2.5.3a