SLAM-seq/GRAND-SLAM of HCT116 (DCP1a KO) cells, , 0hr, replica 2
SLAM-DUNK, in conjunction with the globally refined analysis of newly transcribed RNA and decay rates using SLAM-seq (GRAND-SLAM), was used to analyze SLAM-seq datasets. SLAM-DUNK is automated SLAM-seq data analysis pipeline and features MultiQC plugin for diagnostic and quality assurance purposes. SLAM-DUNK output was used to run GRAND-SLAM. SLAM-DUNK v0.4.3 was used and the following code was used to run this pipeline:  slamdunk all -r /mnt/e/slamseq_run_9_9_2021/hg19_no_alt_analysis_set.fa -b /mnt/e/slamseq_run_9_9_2021/pure_UTR_3_hg19_ensemble.bed -o /mnt/e/slamseq_run_9_9_2021/ /mnt/e/slamseq_run_9_9_2021/sample_file.tsv GRAND-SLAM output includes the proportion and the corresponding posterior distribution of new and old RNA for each gene. GRAND SLAM v2.0.6 version was used and the following code was use to run the pipeline gedi -e Slam -genomic homo_sapiens.75 -prefix test2/24h -progress -plot -D -full -reads bams.bamlist SLAM-DUNK can be found at https://t-neumann.github.io/slamdunk/ and GRAND-SLAM at https://github.com/erhard-lab/gedi/wiki/GRAND-SLAM.