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Workflow for PacBio BCR-ABL1 mutation screening

Step 1. Run 'reads of insert' plugin in SMRT portal

Log on to the SMRT portal. Click on 'Create New' and select the SMRT cell containing the data for the patient to be analyzed. Select 'RS.ReadsOfInsert' under the 'Protocols', assign a job name for the analysis (pb_XXX_X_ccs_reads) and click on the 'Start' button.

Step 2. Store result files on a local computer

Create a new directory named 'pb_XXX_X' using the following commands:

[TODO: add cd and mkdir commands here!]

When the 'RS.ReadsOfInsert' plugin is done, download the FASTA, FASTQ and PDF files to the newly created directory. The files should be renamed to: 'pb_XXX_X_reads_of_insert.fasta', 'pb_XXX_X_reads_of_insert.fastq' and 'pb_XXX_X.pdf'. Running the command 'ls -l' in the directory should give output that look similar to this:

[TODO: add ls -l command here!]

Step 3. Run the BCR-ABL1 mutation screening analysis

[TODO: add R commands here!]

Step 4. Perform QC on the run and analysis

[TODO: add some criteria here]

Step 5. Upload result files into web based system

[TODO: manually upload the fastq and mutation file in a web form. At the same time enter information about the run]