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assignments:rna2018_assignment3

Assignment 3

DSCI512: RNAseq
Due date: November 13, 2016, 10:00am
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Build genome indices for the C. elegans genome

  • Create a new directory called PROJ03_celegansGenome
  • Use what you learned about downloading the yeast genome to download the C. elegans ce11 genome
  • Build hisat2 indices for the C. elegans ce11 genome.
  • Write down everything in your notebook.

Download the entire fasta file for the whole C. elegans genome

  • Write down what you did in your notebook.

Download the chromosome length file for the C. elegans genome

  • Write down what you did in your notebook.

Download the annotation file for the C. elegans genome

  • Write down what you did in your notebook.
  • Try to put the C. elegans annotation file onto summit in the PROJ03_celegansGenome directory

Turn in the following. This can only be submitted as a .txt file or copied and pasted into canvas as .txt documentation. No word files, No fancy text.

1. Using the command ls -alh, list the output (.ht2 files) you generated. For example, here is what it looks like for the yeast example:

-rw-r--r-- 1 erinnish@colostate.edu erinnishpgrp@colostate.edu 7.9M Nov 15 04:36 sc3.1.ht2
-rw-r--r-- 1 erinnish@colostate.edu erinnishpgrp@colostate.edu 2.9M Nov 15 04:36 sc3.2.ht2
-rw-r--r-- 1 erinnish@colostate.edu erinnishpgrp@colostate.edu  161 Nov 15 04:36 sc3.3.ht2
-rw-r--r-- 1 erinnish@colostate.edu erinnishpgrp@colostate.edu 2.9M Nov 15 04:36 sc3.4.ht2
-rw-r--r-- 1 erinnish@colostate.edu erinnishpgrp@colostate.edu 5.2M Nov 15 04:36 sc3.5.ht2
-rw-r--r-- 1 erinnish@colostate.edu erinnishpgrp@colostate.edu 3.0M Nov 15 04:36 sc3.6.ht2
-rw-r--r-- 1 erinnish@colostate.edu erinnishpgrp@colostate.edu   12 Nov 15 04:36 sc3.7.ht2
-rw-r--r-- 1 erinnish@colostate.edu erinnishpgrp@colostate.edu    8 Nov 15 04:36 sc3.8.ht2

2. What is the absolute path to your whole chromosome fasta file (chromFa.tar.gz)?

Example for sc3:
/scratch/summit/erinnish@colostate.edu/DSCI512_RNAseq/PROJ02_yeastGenome/chromFa.tar.gz

3. What is the absolute path to your chromosome sizes file (ce11.chrom.sizes)?

4. What is the absolute path to your annotation file (.gtf)?

Extra challenge: Can you pipe together a series of cut, uniq, and ''sort commands that will count the number of unique gene_id's in your annotation file? How many unique genes are there in the C. elegans genome?

assignments/rna2018_assignment3.txt · Last modified: 2018/11/15 09:31 by erin