From e2fc59bfe105c5e16d688350cdef9edb1e188b9a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Anita=20Sch=C3=BCrch?= Date: Thu, 21 Nov 2019 15:02:01 +0100 Subject: [PATCH] added expl. Moved explanation of -p. Also, adjusted time estimate for download (although still conservative IMO) --- episodes/02-quality-control.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/episodes/02-quality-control.md b/episodes/02-quality-control.md index 751d5f5..0988601 100644 --- a/episodes/02-quality-control.md +++ b/episodes/02-quality-control.md @@ -45,7 +45,11 @@ We are studying a population of *Escherichia coli* (designated Ara-3), which wer The data are paired-end, so we will download two files for each sample. We will use the [European Nucleotide Archive](https://www.ebi.ac.uk/ena) to get our data. The ENA "provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation." The ENA also provides sequencing data in the fastq format, an important format for sequencing reads that we will be learning about today. -To download the data, run the commands below. It will take about 10 minutes to download the files. +To download the data, run the commands below. + +Here we are using the `-p` option for `mkdir`. This option allows `mkdir` to create the new directory, even if one of the parent directories doesn't already exist. It also supresses errors if the directory already exists, without overwriting that directory. + +It will take about 15 minutes to download the files. ~~~ mkdir -p ~/dc_workshop/data/untrimmed_fastq/ cd ~/dc_workshop/data/untrimmed_fastq