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Question: makeTxdbfromUCSC Warning message
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gravatar for Lillyhchen
22 months ago by
Lillyhchen10
United States
Lillyhchen10 wrote:

Hi everyone,

I'm trying to use the makeTxdbfromUCSC() function to create a txdb of exons sorted by genes.  It seems the function runs fine, but I just noticed that when I run the function I get a warning message: "Warning message:
In .extractCdsLocsFromUCSCTxTable(ucsc_txtable, exon_locs) :
  UCSC data anomaly in 19284 transcript(s): the cds cumulative length is
  not a multiple of 3 for transcripts"

Because the coding sequence is not a multiple of 3 for transcripts, could this possibly cause an error in my results because not all the transcripts are created?

Any tips on this or how to fix it would be very appreciated! thank you!

 

Lilly

ADD COMMENTlink modified 22 months ago by Marc Carlson7.2k • written 22 months ago by Lillyhchen10
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gravatar for Marc Carlson
22 months ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:

This warning is really just telling you something about the source data and not about the TxDb.  Since it is expected that a cds length would be divisible by three, the code checks for that and reports to you whenever this doesn't happen.  You can decide what you want to do about it (if anything).  

 

 Marc

ADD COMMENTlink written 22 months ago by Marc Carlson7.2k
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