This step included the adaptor removal as well as the application of a stringent filtering criterion to remove reads with >10% unknown bases and remove low quality reads, i.e. reads that comprise at least 50% low-quality bases.
Reads were trimmed using Trimmomatic36 with default parameters to remove reads containing adapters and reads of low quality.
RNA-seq data were filtered using the following criteria: (1) remove reads containing adapters; (2) remove reads containing N > 10%, where N represents a base that cannot be determined; (3) remove reads containing low-quality (Qscore ≤ 5) bases accounting for more than 50% of the total bases.
Sites with supportive evidence of altered variation in RNA-seq have been extracted from the final vcf file, and ASEReadCounter37 was applied to remove reads with low base quality.
Oxytricha trifallax mitochondrial genomic peptides and bacterial genomes database were downloaded from GenBank as a mapping reference to remove reads which were probably contaminated by mitochondria or bacteria.
Using the active measurement method, the frame remove reads the data frame in the SRAM and sends it to a MAC TxQ according to x for y times.
The clean reads were produced after the raw reads were filtered to the following criteria: remove reads with sequence adaptors; remove reads with more than 10% 'N' bases; and remove low-quality reads, which have more than 50% QA ≤ 10 bases.
Reads were filtered to remove reads containing homopolymer stretches longer than 10 bases, ambiguous bases, reads less than 200 bp in length and reads longer than 275 bp using Mothur.
After filtering to remove reads containing the adapter and poly-N or low quality reads, 36,187,662 and 38,239,937 clean reads remained in the WT and ∆fliC libraries, respectively.
The UDPS data were cleaned to remove reads with PCR and UDPS artifacts while retaining as many high-confidence sequences as possible (see Materials and Methods).
We applied a simple filter to remove reads with low quality colour calls or low mapping scores from the resulting SAM file.
