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assignments:ex13 [2018/11/26 13:16]
dokuroot
assignments:ex13 [2018/11/27 12:56]
dokuroot
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-**3.** Assess the quality of the data using ''​FastQC'':​+**2.** Assess the quality of the data using ''​FastQC'':​
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-**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
  
-For the base name use a descriptive name, For example, for the brain_rep_1 set, use ''​brain1.fastq.gz''​\\+For output file names, use:\\ 
 +trimmed_brain1_P1.fastq.gz\\ 
 +trimmed_brain1_P2.fastq.gz\\ 
 +trimmed_brain1_U1.fastq.gz\\ 
 +trimmed_brain1_U2.fastq.gz\\
  
 //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 //
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-**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: ​
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-**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'​
assignments/ex13.txt · Last modified: 2018/11/27 12:56 by dokuroot