Question: No ht-seq in main Galaxy menu?
gravatar for henrikad
3.3 years ago by
United States
henrikad0 wrote:

Why is there no way in the main Galaxy menu to produce a raw counts matrix (not normalized and not R/ FPKM) from the RNA-Seq alignment to a reference genome?  Some downstream tools (e.g., DESeq2) require a raw counts matrix as input. Any chance to get ht-seq or something analogous included in the menu of NGS:RNA-Seq tools?


rna-seq • 752 views
ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson25k • written 3.3 years ago by henrikad0
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Both of these tools and several others useful for RNA-seq analysis are available as installable tool repositories from the Tool Shed. Use these in a local or Cloudman Galaxy. If choosing Cloudman, keep in mind that AWS offers grants for academic/research/teaching purposes that can help offset compute costs (Galaxy is always free!).

Best, Jen, Galaxy team


ADD COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k
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