Please Help With The Settings For Cufflink, Cuffmerge And Cuffdiff

Question: Please Help With The Settings For Cufflink, Cuffmerge And Cuffdiff

6.3 years ago by

Du, Jianguang • 380 wrote:

Dear All, I am looking for the differential splicing events between cell types. Although I got a lot of helps from Jen and from protocols found online, I am still not sure about some settings for Cufflink, Cuffmerge and Cuffdiff. 1) For Cufflink: There is a setting for Bias Correction. I made the setting as below: Perform Bias Correction: Yes Reference sequence data: Locally cached Did I make the right settings? 2) For Cuffmerge: As for whether use sequence data, I made the setting as below: Use Sequence Data: Yes Choose the source for the reference list: Locally cached Did I make the right settings? 3) For Cuffdiff: There is another choice whether perform Bias Correction, I made the setting as below: Perform Bias Correction: Yes Reference sequence data: Locally cached Did I make the right settings? Thanks. Jianguang

rna-seq cuffmerge • 3.0k views

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modified 6.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.3 years ago by Du, Jianguang • 380

6.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Jianguang, If your input dataset(s) have a genome assigned ("database") and that genome is local to Galaxy (I believe this is true for your data, mm9, correct?), then using bias correction would be an advantageous option to make use of according to our experience and the tool authors in the Cufflinks manuals/protocols/publications. That said, the choice of whether or not to use Bias correction would be ultimately up to you (a test using and not using could help with this decision). From what I know, it is generally considered best practice to use it when available. Custom genomes can also be used with bias correction, but require a different way of setting options and database assignments. Using no reference genome is also possible (and therefore no bias correction), again with different settings. The tool form has general instructions around this as does the RNA-seq FAQ under Shared Data -> Published Pages and the Custom genome wiki. In addition, there are several prior posts with Q/A on the topic on the mailing list (a search would bring up the settings for others reading this post that are curious). Anything that remains unclear we can help with (send a new Q to the list) and we can adjust the wiki, etc. to be more specific if not covered already. http://galaxyproject.org/search/mailinglists Take care, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

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