makeTxdbfromUCSC Warning message
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Lillyhchen ▴ 10
@lillyhchen-8385
Last seen 7.4 years ago
United States

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

MakeTXDCfromUCSC GenomicFeatures warning • 1.5k views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 6.3 years ago
United States

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

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