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assignments:ex13 [2018/11/26 11:00]
dokuroot
assignments:ex13 [2018/11/27 12:56] (current)
dokuroot
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-**Note:** this pipeline is no longer updated and has been replaced with a more efficient and accurate pipeline, however, we will use the original Tuxedo pipeline because there is far more support currently available for it and it has fewer bugs to contend with. The new and improved pipeline consists of a similar suite of tools: HISAT, StringTie, and Ballgown. ​+**Note:** this pipeline is no longer updated and has been replaced with a more efficient and accurate pipeline, however, we will use the original Tuxedo pipeline because there is far more support currently available for it and it has fewer bugs to contend with. The new and improved pipeline consists of a similar suite of tools: HISAT, StringTie, and Ballgown. ​See https://​www.nature.com/​articles/​nprot.2016.095
  
 ====OUTLINE==== ====OUTLINE====
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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 -phred33 ​'​input_fastq_1'​ '​input_fastq_2'​ 'output_fastq_paired_1' 'output_fastq_unpaired_1' 'output_fastq_paired_2' 'output_fastq_unpaired_2' ILLUMINACLIP:/​usr/share/trimmomatic/​adapters/​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 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/ex13.1543255234.txt.gz · Last modified: 2018/11/26 11:00 by dokuroot