README.md

1. Sample raw data: enclosed is a text file with dataset download links.
2. File types for inputs and outputs at each step (particularly for FASTQC and TrimGalore (first two steps) operations)

Enclosed as a table below (also enclosed the corresponding excel file):

S.No. Analysis stage Tool used Input file type Code Output data type 
1 Quality check FastQC fq / fastq ./fastqc *fastq.gz text, html QC reports 
2 Quality trimming TrimGalore fq / fastq trim_galore --gzip --fastqc --max_n 2 --paired --length 50 SRR11862696_1.fastq.gz SRR11862696_2.fastq.gz fq; fastq