I am learning RNA seq analysis. Firstly, I am using Prinseq lite for preprocessing of data.
I used command:
perl prinseq-lite.pl –fastq read_1.fastq -fastq2 read_2.fastq -out_format 5 -min_len 50 -min_qual_mean 25
I got three output files in same folder for each data file. These are
Further, the size of
_prinseq_good_ is greater than input data file. Is it OK?
Please suggest me that which file could I use for downstream analysis?