HISAT2 (option for 50 % of attendees)

  1. create a new history and name it HISAT2
  2. Import the 11 datasets from the RNAseq data library to this HISAT2 history, plus the Drosophila_melanogaster.BDGP6.95.gtf file
  3. Select the HISAT2 tool with the following parameters to map your reads on the reference genome:
    1. Source for the reference genome: Use a builtin genome
    2. Select a reference genome : dm6
    3. Is this a single or paired library: Single-End
    4. FASTA/Q file :
      • GSM461176_untreat_single.fastq.gz
      • GSM461179_treat_single.fastq.gz
      • GSM461182_untreat_single.fastq.gz
    5. Specify strand information: Unstranded
    6. Summary options
      • Output alignment summary in a more machine-friendly style.: YES
      • Print alignment summary to a file.: YES
    7. Leave other settings as defaults
  4. Execute

Redo the HISAT2 run for paired-end files

  1. Rerun the HISAT2 tool with the following parameters to map your reads on the reference genome:
    1. Source for the reference genome: Use a builtin genome
    2. Select a reference genome : dm6
    3. Is this a single or paired library: Paired-End
    4. FASTA/Q file #1:
      • GSM461177_1_untreat_paired.fastq.gz
      • GSM461178_1_untreat_paired.fastq.gz
      • GSM461180_1_treat_paired.fastq.gz
      • GSM461181_1_treat_paired.fastq.gz
    5. FASTA/Q file #2:
      • GSM461177_2_untreat_paired.fastq.gz
      • GSM461178_2_untreat_paired.fastq.gz
      • GSM461180_2_treat_paired.fastq.gz
      • GSM461181_2_treat_paired.fastq.gz
    6. Specify strand information: Unstranded
    7. Leave other settings as defaults (since you are redoing a run)
  2. Execute

Rename your datasets !

You need now to rename you datasets to facilitate your downstream analysis.

Be quiet and focus ! No hurry, this is an important task in the analysis.

  1. Search and select datasets with HISAT2

  2. Click on the info icon of both (BAM) and Mapping summary files

  3. Copy the name or one of the two names of the datasets as shown bellow

  4. Now click on the pencil icon of the same dataset
  5. Paste your text in the Name field of the dataset
  6. Edit your text as follow for Mapping summary files

  7. Edit your text as follow for (BAM) files

  8. repeat ad lib for all Mapping summary and (BAM) files