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Partek Flow Documentation

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Why are there decimal values in the Partek E/M quantification output?


The Partek E/M quantification algorithm can give decimal values because of multi-mapping reads (the same read potentially aligning to multiple locations) and overlapping transcripts/genes (a read that maps to a location with multiple transcripts or genes at that location). In these scenarios, the read count will be split.

For example, if a read maps to two potential locations, then that read contributes 0.5 counts to the first location and 0.5 counts to the second location. Similarly, if a read maps to one location with two overlapping genes, then that read contributes 0.5 counts to the first gene and 0.5 counts to the second gene.

If you need to remove the decimal points for downstream analysis outside of Partek Flow, you can round the values to the nearest integer.

 

Why can't I view PCA on Google Chrome and I am being pointed to WebGL instructions?

If you are using Google Chrome, some graphics card (particularly in older Mac laptops) are not supported and they affect the ability to run WebGL (needed to display PCA). You may wish to use a different browser (Mozilla Firefox) or you can try running Google Chrome while ignoring any blacklisted hardware:

  • For Mac, this is the command: /Applications/Google\ Chrome.app/Contents/MacOS/Google\ Chrome --ignore-gpu-blacklist
  • Here is a video of a workaround and also creating an automated tool in a Mac: https://customer.partek.com/tutorials/ChromeWebGLWorkaround.mp4 (02:55)
  • The app created in the video is available for download here (ChromeWebGL.app.zip). Unzip and make sure to exit Google Chrome complete before running the app.

I have two projects that I ran separately. I want to combine the two projects without repeating the alignment step. How can I combine the aligned reads?

Create a third project. Import two sets of BAM files.

Project 1 - In Data Tab, take note of your project output folder. Also note the aligner that you used. 

Project 2 - In Data Tab, take note of your project output folder. Also note the aligner that you used. 

Project 3 - Create project. Import Data > Automatically create samples from files > Find the project output folder of Project 1 (should be in Partek Flow server) > Find the folder for the aligner you used > Within that folder should be the BAM files > Select the BAM files > Create sample. Repeat same process for Project 2.

Now you will have all samples as one data node (aligned reads) in Project 3. You can proceed with downstream analysis (normalization, differential gene expression, etc).

Why is the number of variants listed in the variant reports and summarize cohort mutations report different?

For variants with multiple alternative alleles, the variant has one row for all alternative alleles, while the summarize cohort mutations report lists each alternative allele on a separate rows. The number of variants listed at the top of the each report is calculated from the number of rows in the report.  


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