When I did fastqc analysis on my original fastq files, the encoding that I can see in the biostatistics was sanger/illumina 1.9. But when I did the trimmomatic on those fastq files to trim low quality bases followed by fastqc analysis on the trimmed fastq files the encoding in the biostastics was Illumina 1.5. Why is it so?
I made sure that the ASCII characters are not messed up with trimmomatic parameters. However, I am surprised to see the change in the encoding. My only concern is will it affect any subsequent downstream analysis??