5' isoform-specific m6A quantification with CROWN-seq

An updated version of 5' isoform-specific iternal m6A analyses of CROWN-seq. File structures: File Description [cell_line_replicate].TSS_m6A.txt.all.cov20.annot_exon.csv A file containing all the read counts for each TSS-A-site pairs. The distance between the A site and cap, as well as the distance between the A site and the 3' exon end, are included. NO filters are applied except for a minimum coverage of 20. See https://github.com/jhfoxliu/TSS_m6A about how the files were generated [cell_line_replicate]_merged.csv If mulitple replicates are available, the reads of the same TSS-A-site pair were merged to increase sequencing depth. [cell_line_replicate]_merged.cov50.csv Based on [cell_line_replicate]_merged.csv, only TSS-A-site pairs with at least 50 reads were selected. [cell_line_replicate]_merged.cov50.max_0.2.csv Based on [cell_line_replicate]_merged.cov50.csv, onlyt TSS-A-site pairs where at least one isoform exhibit minimum stoichiometry of 0.2 were selected. [cell_line_replicate]_merged.cov50.max_0.2.DRACH.csv Based on [cell_line_replicate]_merged.cov50.max_0.2.csv. This is the high-confidence TSS-m6A-site list. Only sites in DRACH motif were used. About the high-confidence TSS-m6A-site list [cell_line_replicate]_merged.cov50.max_0.2.DRACH.csv: Columns: chr Chromosome id TSS TSS position, 1-based, hg38. Target m6A site position, 1-based, hg38. strand Strand. A Number of A (i.e., non-converted) reads. Cov Number of all reads. dist_5p Distance to 5' end. dist_3p Distance to the nearest 3' exon end. level m6A level, equals A/Cov. seq The 2-nt long flanking sequence. DRACH If TRUE, the site is located in a DRACH motif. max_level The maximum m6A level of the site at 5' isoform level.