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assignments:assignment4key

Assignment 4 Key

1. 
  A. gene_id
  B. 
    1st cut: This step extracts the "feature" information, the 9th tab-delimited column of the file saccer3_annotation.gtf
    2nd cut: This pulls out the first semi-colon-delimited elment, the gene_id, that was passed from the previous cut command
    3rd sort: This sorts all the gene_id's
    4th uniq: This removes redundant gene IDs
    5th wc - l: This counts the number of lines


2. 
  A. cut -f 3 saccer3_annotation.gtf | sort | uniq
  B. 
    cut -f 3 saccer3_annotation.gtf > features_tmp.txt
    sort features_tmp.txt > features_sorted_tmp.txt
    uniq features_sorted_tmp.txt


3. 
  A. login node
  B. login node, compile node
  C. compute nodes
  
  
4. 
  A. bowtie -p 1 file.fastq  OR  sbatch bowtie_align.sh
  B. #SBATCH --time=0:30:00
  C. # compresses a genome
  D. tells slurm to allot 1 core for the job
  
  
Quesiton 5
  A. ssh -l erinnish@colostate.edu login.rc.colorado.edu
  B. ssh scompile
  C. sbatch bowtie_align.sh
  D. squeue -u $USER
  
assignments/assignment4key.txt · Last modified: 2018/09/10 09:19 by erin