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Question: Missing Information with transcriptlengthsfunction
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gravatar for michael.soutschek
9 months ago by
michael.soutschek0 wrote:

Good evening,

as others reported previously, I had Problems today in creating a txdb object from Biomart.

> txdb <- makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL",
+                               dataset="rnorvegicus_gene_ensembl")
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped)
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning messages:
1: In download.file(url, destfile, quiet = TRUE) :
  InternetOpenUrl failed: 'The login request was denied
'
2: call dbDisconnect() when finished working with a connection 
3: In .makeTxDb_normarg_chrominfo(chrominfo, transcripts$tx_chrom,  :
  chromosome lengths and circularity flags are not available for this TxDb object

One could work with the object, but it gives for example only incomplete information upon using the transcriptlengths function:

leng <- transcriptLengths(txdb, with.cds_len = TRUE)

The value of most of the genes is 0 in the resulting data.frame. After trying for a while with a Windows computer, I continued with a Mac. There I didn't get the error messages upon creating the txdb, but the resulting data.frame contained still mostly 0s.

​I know that this extraction has worked previously very nicely! If you have any suggestions or know where the error could be, please let me know, I would be very grateful!

​Best, Michael

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