The following table shows important quality control metrics for each sample. Two libraries are made for each sample, one containing sequences immunoprecipitated with the antibody of interest (IP), and one RNA-seq background control (input). For each library, one row is included that lists the metrics for each library. The identity of the library is included in the "IP or input" column. The following columns describe the processing of the libraries:

1.  Initial reads: the number of sequenced reads for each library.
2.  % Pass trim: reads first underwent adapter trimming to remove both adapters and sequences shorter than 18 nucleotides. The percentage of sequenced reads that passed this trimming step is listed in this column.
3.  % Repetitive elements: trimmed reads are aligned to Eclipsebio's custom database of repetitive elements. This database includes rRNAs, tRNAs, snoRNAs, and other features. The percentage of trimmed reads that were filtered is listed in the column.
4.  % Uniquely aligned to the genome: the remaining reads from the repetitive element filtering were aligned to the genome, and the percent of those reads that map uniquely to the genome is listed in this column.
5.  % PCR duplicates: PCR duplicates were defined as uniquely mapped reads that map to the same read coordinates and have an identical unique molecular identifier (UMI). The percentage of mapped reads that were identified as PCR duplicates is included in this column.
6.  Final reads: this column lists the number of uniquely mapped, deduplicated reads that were used for this analysis.
7.  Clusters: Clusters were defined as regions on genes within the IP sample that contain an enrichment of read coverage. These clusters were identified by the peak called CLIPper. The number of clusters called in each IP sample is listed in this column. Clusters are not called for input samples.
8.  Input-normalized peaks: For every cluster called, an IP vs. input log2 fold change and associated p-value were calculated using the Yates' Chi-square test or Fisher Exact test if read counts were < 5. Peaks were defined as clusters with log2 fold enrichment > 3 and p-value < 0.001. The number of peaks identified for each IP sample is listed in this column. Peaks are not called for input samples.
9.  Single nucleotide sites: Single nucleotide sites were identified using the tool PureCLIP. Called sites are enriched in the IP sample over the corresponding input control sample.
10.  Filtered m6A sites: Single nucleotide sites filtered for the following criteria: score ≥ 10, on an "A" nucleotide, and intersects with a significantly enriched m6A peak.