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assignments:ex13 [2018/11/26 11:19]
dokuroot
assignments:ex13 [2018/11/27 12:56] (current)
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, such as for brain_rep_1, 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'​
  
-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/ex13.1543256398.txt.gz · Last modified: 2018/11/26 11:19 by dokuroot