Here are some Frequently Asked Questions about Partek® Flow® software based on real support calls.
Why can’t I find the RPKM method on the normalization menu (I see FPKM)?
When working with paired data it should be the case that FPKM is available, and when working with single end data RPKM should be available. These metrics are essentially analogous, but based on the underlying method used for calculation (accounting for two reads mapping to 1 fragment and not counting twice for paired end data). Here is a simple description of the differences in calculation between RPKM and FPKM: http://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained.
Why don't you have RPM in your normalization?
RPM (reads per million) is the same as Total Count. Please use Total Count.
What is a canonical transcript?
For genes with multiple transcripts, one of the transcripts is picked as the canonical transcript. Based on the UCSC definition from the table browser,
knownCanonical - identifies the canonical isoform of each cluster ID, or gene. Generally, this is the longest isoform.
Why is my PCA not displaying and I am asking to enable WebGL in my browser?
If you are using Google Chrome, some graphics card (particularly on older Mac laptops) are not supported to use WebGL. This affects your ability to use PCA. You may wish to use a different browser (Mozilla Firefox) or you can try running Google Chrome and ignorning any blacklisted hardware:
- For Mac, this is the command: /Applications/Google\ Chrome.app/Contents/MacOS/Google\ Chrome --ignore-gpu-blacklist
- Here is the video of a workaround and also creating an automated tool in Macs: https://customer.partek.com/tutorials/ChromeWebGLWorkaround.mp4 (02:55)
Additional Assistance
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
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