CODEWITHSUNDEEP
bashshellfastqgoogle-genomics
Luffy
Luffy

Reputation: 1

Run of Mutiple fastq files for fastqc analysis

I would run the following code for multiple fastq files in a folder. In a folder I have different fastq files; first I have to read one file and perform the required operations by activating the miniconda , then store results in a separate file. fastq and then read second file, perform the same operations and save results in new 2nd file.fastq using the bash script and python script

#!/bin/bash

# directory of with mutiple fastq files#
FILES= " /home/folder/sample"

for f in $ FILES

do 
  conda activate FAST_qc    # actibvating the miniconda
  echo "Process the file $f
  mkdir "$f"                # making directory
  fastqc "$f"               # task to perform
done

Upvotes: 0

Views: 308

Answers (0)

Related Questions