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assignments:grep [2018/11/15 11:31]
dokuroot
assignments:grep [2018/11/15 13:09] (current)
dokuroot
Line 54: Line 54:
  
 **7.** Examine the file using ''​more''​. ​ Do the chromosome IDs match the chromosome IDs in the gtf file?  **7.** Examine the file using ''​more''​. ​ Do the chromosome IDs match the chromosome IDs in the gtf file? 
 +
 +====Alternative Approach====
 +**1.** Open Cyberduck or Filezilla. \\
 +
 +**2.** Download the genome annotations for human genome release hg39 from ensembl: \\
 +
 +path: ''​ftp://​ftp.ensembl.org/​pub/​release-90/​gtf/​homo_sapiens/''​ \\
 +file: ''​Homo_sapiens.GRCh38.90.gtf.gz''​ \\
 +
 +**3.** Extract lines containing chromosome 22 features using ''​grep''​.\\
 + 
 +**4.** Extract exon entries using ''​grep''​.\\
 +
 +**5.** Download chromosome 22 DNA sequence from ensembl: \\
 +
 +path: ''​ftp://​ftp.ensembl.org/​pub/​release-90/​fasta/​homo_sapiens/​dna/''​ \\
 +file: ''​Homo_sapiens.GRCh38.dna.chromosome.22.fa.gz''​
 +
 +**6.** Rename sequence ID to 22 using ''​sed''​. ​
assignments/grep.txt ยท Last modified: 2018/11/15 13:09 by dokuroot