The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Rationale:


Trimmomatic-programmable-0.38 app provides access to all trimmers that Trimmomatic can use. It uses a line-by-line text file for programming the trimming profile. Trimmomatic is commonly used for trimming stretches of sequences that are extraneous contaminants or of low quality. There are many trimmers available to use within a single run of Trimmomatic. For this app, using a trimmer only requires including it (with proper syntax) in the trimmer settings file..

Trimmomatic-programmable-0.38 is invoked using the following:

  1. Paired-end reads:
    1. FASTQ Files (Read 1)
    2. FASTQ Files (Read 2)

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      Make sure the paired-end reads have R1 and R2 in them. For example test_R1.fq.gz and test_R2.fq.gz otherwise the app will fail to process the paired-end readsEnter a folder of sequencing files (Mandatory)

  2. Single end reads

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    One of the Paired-end reads or Single-end reads should be filled for the app to work

  3. Trimer file (Mandatory)

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    Input below a trimmer file in basic text format. You can create one in the Data window by clicking on the File menu and choosing Create > Plain text file. Enter line by line all the trimmer settings you want to use with Trimmomatic. See http://www.usadellab.org/cms/?page=trimmomatic for more details

  4. Adapters (Optional)
    1. ILLUMINACLIP adapter sequence file
    2. Adapter clip seed mismatches (Default is 2)
    3. Adapter clip palindrome clip threshold (Default is 30)
    4. Adapter clip simple clip threshold (Default is 10)
  5. Settings
    1. Phred33 (Default is Phred 64)
    2. Number of CPUs (Default is 4)
  6. Output
    1. Output Folder name (Default is trimout)

Test Data

Run Trimmomatic-programmable-0.38 as following:

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All files are located in the Community Data directory of the iPlant Discovery Environment at the following path: Community Data > iplantcollaborative > example_data > trimmomatic-0.33 > inputs (/iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs)

  1. Paired-end reads: Select the files from the directory - /iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs/testfiles
    1. FASTQ Files (Read 1) - EP1_C1_CGATGT_L004_R1_001.fq.gz, sample_1_R1_001.fq.gz and sample_2_R1_001.fq.gz
    2. FASTQ Files (Read 2) - EP1_C1_CGATGT_L004_R2_001.fq.gz, sample_1_R2_001.fq.gz and sample_2_R2_001.fq.gz

  2. Single end reads

  3. Trimer file (Mandatory) - /iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs/testfile_trimmomatic.txt

  4. Adapters (Optional)
    1. ILLUMINACLIP adapter sequence file - /iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs/Adapters.fa
    2. Adapter clip seed mismatches (Default is 2) - Leave 
    3. Adapter clip palindrome clip threshold (Default is 30)
    4. Adapter clip simple clip threshold (Default is 10)
  5. Settings
    1. Phred33 (Default is Phred 64)
    2. Number of CPUs (Default is 4)
  6. Output
    1. Output Folder name (Default is trimout)


Please work through the documentation and add your comments on the bottom of this page, or click the intercom button on this page. 

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