Day 1 - ryandkuster/EPP_575_RNA_25 GitHub Wiki

Agenda

Syllabus

Day 1 recording

Time	Lecture	Lab	Instructor
9:00	Introduction and Syllabus		Ryan
9:10
9:20
9:30	01 Introducting the Shell	SWC 1	Ryan
9:40
9:50	02 Navigating Files and Directories	SWC 2	Patrick
10:00
10:10	10 minute break	:coffee:
10:20
10:30	03 Working with Files and Directories	SWC 3	Patrick
10:40
10:50	File formats: fasta
11:00	04 Pipes and Filters	SWC 4	Patrick
11:10
11:20	File formats: fastq

Day 1 Assignment:

Send the following to [email protected] by the end of the day. Please answer all parts of the questions and keep in the same order as written below.

1. From the EPP_575_RNA_25/data/practice_data directory, get the length (number of lines) for each of the files with _subset in the name. Write this output to a file called subset_lengths.txt.
2. Provide the command that would achieve the above.
3. If you run sort on the file GCA_000001735.2_subset.fna, does the header line end up at the beginning or the end of the file?
4. Based on the file suffices ".fastq", ".fna", and ".gff3", what kind of information do you expect to find in these files?
5. What is the most useful thing you learned today? Why?