GSM9099819: LR1-WT_biological_replicate_3_technical_replicate2; Chlorocebus; RNA-Seq
The total RNA was then extracted from the cells using E.Z.N.A. Total RNA Kit I (Omega bio-tek) The A-to-I editing analysis pipeline was referred to previous study26 with some modifications. Raw reads were cleaned using FASTP47. Ten bases of 5' and 3' were trimmed and reads with more than 20% of unqualified bases were removed. The mean quality per base was fixed at a phred-score of 25. The reads that were shorter than 100 nt were discarded. The cleaned reads were mapped to the reference sequence using BWA48 aln (bwa aln -t 20) and mem (bwa mem -M -t 20 -k 50). The unmapped reads were extracted for editing site calling as described in the published study26. Editing site calling was performed by subsampled each library to the same reads' depth. To identify edited reads, read was specially required to have a minimum number of edited sites >= 4 (with either A-to-G or T-to-C sites in a read). The putative misaligned reads matching any of the criteria as shown in the study26 were also excluded. Only reads with the number of mismatch and low-quality A-to-G/T-to-C sites <=2 were considered as edited reads. For each sample, the editing index was defined as number of editing sites from edited viral reads divided by the total number of viral reads in our study. The editing level was quantified by calculating the percentage of editing counts out of total reads at each position.