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Question: How to Get Transcript Length for Ref-seq genes
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gravatar for joseph.landry
7 weeks ago by
joseph.landry • 0
joseph.landry • 0 wrote:

Hi All,

I would like to calculate FPKM for the gene output I get from an EdgeR analysis of RNA-Seq data. As part of the output I get CPM but I want to convert to FPKM. To do so I need the processed transcript length. With the Ref-Seq identifier I can down load from UCSC the Ref-seq table, but it does not have processed transcript length as a column. It has exons, and their start and end, which I could use to determine processed transcript length, but there has got to be an easier way.

Best,

Joe
rna-seq • 75 views
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modified 7 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 7 weeks ago by joseph.landry • 0
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gravatar for Jennifer Hillman Jackson
7 weeks ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The CDS start/end included in the primary table is how UCSC defines that length. It is not contained in a distinct column as far as I know (only the full transcript length is pre-calculated, and it includes the UTR regions).

Once you have the refGene table in Galaxy, it is one step to subtract the CDS start from the end to produce the length value. Use the too: Compute an expression on every row. Because the data has a 0-based start, you don't need to "add +1" to the math -- just subtract the two values.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 7 weeks ago by Jennifer Hillman Jackson ♦ 25k
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