1. To display a file in the terminal window:
$ cat filename.fastq
Note that if the file is very large it will fly by you on the screen and may take a while to get to the bottom.
2. To search a data file for a specific string:
$ grep "literal_string" filename.fastq
Example, to search the sequence file mydata.fastq for a specific barcode "ACAAGCTA"
$ grep "ACAAGCTA" mydata.fastq
3. Use the "*" to check for string in multiple files of the same type:
$ grep "GCCAAGAC" *.fastq
4. Or to search recursively in all files in a directory and subdirectory:
$ grep "GCCAAGAC" *
For more uses of the "grep" command, click here.