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13 changes: 13 additions & 0 deletions episodes/04-redirection.md
Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,19 @@ directory:
$ cd ~/shell_data/untrimmed_fastq
```

Let's look for lines that contain `ACGT`.

```bash
$ grep ACGT SRR098026.fastq
```

To get only the number of lines with `ACGT`, we can use the `-c` flag.
This is useful if you are unsure about the number of lines that will be found.

```bash
$ grep -c ACGT SRR098026.fastq
```

Suppose we want to see how many reads in our file have really bad segments containing 10 consecutive unknown nucleotides (Ns).

::::::::::::::::::::::::::::::::::::::::: callout
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