Q&A added during the NGS RNASeq data analysis

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Please find here questions raised during the session with some element of answer found with Dr G

[ Main_Page | NGS_data_analysis ]


How many reads do I need for each replicate in my RNASeq project?

This is another central and still controversial question in NGS analysis. The answer depends on the aim of the experiment, the type of NGS applied, and the complexity of the data. Some elements of answer can be found here[1] and in linked pages.

What software or method can I use to analyze differential spicing?

Numerous software are being developed to assess this specific question. Keep in mind that this is on eof the most sofisticated part of RNA Seq and is not yet standardized. You will find a number of posts out there and could start by reading seqanswers threads like [2] and the therein referred non-exhaustive package list [3]. Another Wikipedia page to locate interesting RNA-Seq resources [4].

How data can I upload to Galaxy (Main)

This is indeed a limitation but has recently been improved. Please refer to the Galaxy wiki for more info on how to upload your data or better how to link it via FTP to the Galaxy platform [5]. Please keep in mind that this may not fully apply to the BITS Galaxy instance.

  1. http://www.rna-seqblog.com/how-many-reads-are-enough/
  2. http://seqanswers.com/forums/showthread.php?t=29661
  3. http://seqanswers.com/forums/showthread.php?t=26043
  4. http://en.wikipedia.org/wiki/List_of_RNA-Seq_bioinformatics_tools
  5. https://wiki.galaxyproject.org/FTPUpload?action=show&redirect=Learn%2FUpload+via+FTP

[ Main_Page | NGS_data_analysis ]