GRAND-SLAM analysis of simulated nucleotide conversion in QuantSeq data sets for grandRescue (Q6690166)

These are processed data sets from the simulation of nucleotide conversions (TC) 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