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assignments:ex10 [2017/10/27 14:27]
dokuroot
assignments:ex10 [2018/11/05 15:14] (current)
dokuroot
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-===== Small RNA Data Analysis Part 1: quality control and read mapping =====+===== Small RNA data analysis (part 1): quality control and read mapping =====
  
 \\ Document the exercise in your electronic lab notebook. ​ \\ \\ Document the exercise in your electronic lab notebook. ​ \\
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 NOTE: text in quotes within commands must be changed based on your directory and naming of files. \\ \\ NOTE: text in quotes within commands must be changed based on your directory and naming of files. \\ \\
  
-**1.**  ​Download the small RNA data from the montgomery lab server using ''​Cyberduck''​ or ''​FileZilla''​The path to the folder containing the data is ''​Documents/​SmallRNA_Data/​prg1'' ​\\+**1.**  ​Open a terminal window. \\
  
-**2.** Change into the ''​prg1''​ directory.\\+**2.** Change into the ''​prg1''​ directory: ''/​Users/​bz360/​Documents/​SmallRNA_data/​prg1''​.\\
  
 **3.** There are two small RNA libraries: 1) ''​wt_fastq.txt.gz''​ and 2) ''​prg-1_fastq.txt.gz''​. Examine the contents of the two files using ''​zmore''​. \\ **3.** There are two small RNA libraries: 1) ''​wt_fastq.txt.gz''​ and 2) ''​prg-1_fastq.txt.gz''​. Examine the contents of the two files using ''​zmore''​. \\
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 **5.** Examine the fastq files in ''​FastQC''​. How many reads are there in each library and what is the read length? Record this information in your lab notebook. \\ **5.** Examine the fastq files in ''​FastQC''​. How many reads are there in each library and what is the read length? Record this information in your lab notebook. \\
  
-**6.** Use ''​Trimmomatic''​ to remove adapter sequences and reads shorter than 16 nt:+**6.** Use ''​Trimmomatic''​ to remove adapter sequences ​and filter poor quality reads and reads shorter than 16 nt:
  
-  $ trimmomatic SE -phred33 ​'​input_file'​ '​output_file'​ ILLUMINACLIP:/​Users/​bz360/​Documents/​Trimmomatic_Files/​TruSeq-smallRNA.fa:​2:​30:​10 MINLEN:16+  $ trimmomatic SE '​input_file'​ '​output_file'​ ILLUMINACLIP:/​Users/​bz360/​Documents/​Trimmomatic_Files/​TruSeq-smallRNA.fa:​2:​30:​10 MINLEN:​16 ​AVGQUAL:30
  
 What proportion of reads were dropped? What proportion of reads were dropped?
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   $ bowtie2-build '​genome_input_file.fa'​ '​genome_name'​   $ bowtie2-build '​genome_input_file.fa'​ '​genome_name'​
  
-**9.** Create a new folder within the **prg1** directory called ​**bowtie_cel** using ''​mkdir''​. Move all the files related to the bowtie index and the fasta formatted genome sequence into the **bowtie_cel** folder using ''​mv'':​+**9.** Create a new folder within the ''​prg1'' ​directory called ​''​bowtie_cel'' ​using ''​mkdir''​. Move all the files related to the bowtie index and the fasta formatted genome sequence into the ''​bowtie_cel'' ​folder using ''​mv'':​
  
   $ mv c* bowtie_cel   $ mv c* bowtie_cel
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 **10.** Map reads from each adapter-trimmed library (wt and prg-1 from step 6) to the C. elegans genome using ''​Bowtie2''​. While waiting on bowtie, if you haven'​t done so already, examine the original and trimmed fastq files in ''​FastQC''​. **10.** Map reads from each adapter-trimmed library (wt and prg-1 from step 6) to the C. elegans genome using ''​Bowtie2''​. While waiting on bowtie, if you haven'​t done so already, examine the original and trimmed fastq files in ''​FastQC''​.
  
-  $ bowtie2 -x '​path_to_bowtie_index/​prefix'​ -U '​fastq_file_name'​ -S 'strain.sam'+  $ bowtie2 -x '​path_to_bowtie_index/​prefix'​ -U '​fastq_file_name'​ -S 'sampleID.sam'
    
-NOTE: record the total number of reads and total mapped reads for each library in your lab notebook.+NOTE: record the total number of reads and total mapped reads for each library in your lab notebook:
 \\ \\
 > Total Reads wt: > Total Reads wt:
assignments/ex10.1509136065.txt.gz ยท Last modified: 2017/10/27 14:27 by dokuroot