GRAND-SLAM analysis of simulated nucleotide conversion in QuantSeq data sets for grandRescue

These are processed data sets from the simulation of nucleotide conversions (T>C) in QuantSeq reads for the purpose of investigating 4sU-induced mapping impairment by read lengths and library preparation methods and the potential of grandRescue to alleviate these effects. The original data set is from: Lee, J. W. et al. (https://doi.org/10.1038/s41586-019-1004-y) GEO Accession: GSE109480 (Samples: GSM2944116 – GSM2944120) The zip files contain the full output from the processing pipeline (including the mapped reads, the scripts to run the pipeline and the output) before and after rescue. 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. Software versions: gedi toolkit 1.0.5 GRAND-SLAM 2.0.7 STAR version 2.7.10b