User Tools

Site Tools


assignments:ex13

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Next revision Both sides next revision
assignments:ex13 [2018/11/26 11:21]
dokuroot
assignments:ex13 [2018/11/27 12:54]
dokuroot
Line 44: Line 44:
 \\ \\
  
-**3.** Assess the quality of the data using ''​FastQC'':​+**2.** Assess the quality of the data using ''​FastQC'':​
 \\ \\
  
Line 54: Line 54:
 \\ \\
     ​     ​
-**4.** Trim adapter sequences and quality filter the RNA-seq data (fastq files) using ''​Trimmomatic'':​+**3.** Trim adapter sequences and quality filter the RNA-seq data (fastq files) using ''​Trimmomatic'':​
   ​   ​
 Trim adapter sequences and quality filter each dataset using Trimmomatic (you will run trimmomatic 6 times in total). Trim adapter sequences and quality filter each dataset using Trimmomatic (you will run trimmomatic 6 times in total).
  
-  $ trimmomatic PE '​input_fastq_1'​ '​input_fastq_2'​ 'ouptut_file_base_name' ILLUMINACLIP:/​Users/​bz360/​Documents/​TruSeq3-PE.fa:​2:​30:​10 LEADING:3 TRAILING:3 SLIDINGWINDOW:​4:​15 MINLEN:36 +  $ trimmomatic PE '​input_fastq_1'​ '​input_fastq_2'​ 'trimmed_P1'​ '​trimmed_P2'​ '​trimmed_U1'​ '​trimmed_U2' ILLUMINACLIP:/​Users/​bz360/​Documents/​TruSeq3-PE.fa:​2:​30:​10 LEADING:3 TRAILING:3 SLIDINGWINDOW:​4:​15 MINLEN:​36 ​–baseout '​output_file_base_name'​
  
-For the base name use a descriptive nameFor example, for the brain_rep_1 set, use ''​brain1.fastq.gz''​\\+For output file namesused:\\ 
 +trimmed_brain1_P 
 +trimmed_brain2_P 
 +trimmed_brain1_U 
 +trimmed_brain2_U
  
 //See the Trimmomatic manual for a detailed description of options: http://​www.usadellab.org/​cms/​uploads/​supplementary/​Trimmomatic/​TrimmomaticManual_V0.32.pdf // //See the Trimmomatic manual for a detailed description of options: http://​www.usadellab.org/​cms/​uploads/​supplementary/​Trimmomatic/​TrimmomaticManual_V0.32.pdf //
Line 70: Line 74:
 \\ \\ \\ \\ \\ \\
  
-**5.** Assess the quality of one of the datasets after quality filtering using ''​FastQC'':​+**4.** Assess the quality of one of the datasets after quality filtering using ''​FastQC'':​
  
 In FastQC: ​ In FastQC: ​
Line 77: Line 81:
 \\ \\
  
-**6.** Create a ''​bowtie index''​ for the human chromosome 22 sequence: \\+**5.** Create a ''​bowtie index''​ for the human chromosome 22 sequence: \\
  
  $ bowtie2-build '​sequence.fa'​ '​prefix'​  $ bowtie2-build '​sequence.fa'​ '​prefix'​
  
-The chr22 sequence ​is in the ''​brain_data''​ folder: ''​hg38_chr22.fa''​. \\+The chr22 sequence ​should ​in the ''​brain_data''​ folder: ''​Homo_sapiens.GRCh38.dna.chromosome.22.fa''​. 
 +\\ 
 +You will need to decompress the file if it has the ''​.gz''​ extension. ​ \\ 
 +\\ 
 +If you don't have the chromosome sequence, you can download it here: 
 +\\ 
 +ftp://​ftp.ensembl.org/​pub/​release-94/​fasta/​homo_sapiens/​dna/​ 
  
 For the bowtie prefix, use ''​chr22''​.\\ For the bowtie prefix, use ''​chr22''​.\\
assignments/ex13.txt · Last modified: 2018/11/27 12:56 by dokuroot