Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

Hi Thomas, Thanks for the quick fix. Sonali. On 10/25/2015 1:06 PM, Thomas Girke wrote: I fixed this in systemPipeR versions 1.4.3/1.5.3. The reason for this error was that the tx_type column contains only NA values when a txdb is generated with makeTxDbFromUCSC(). Returning here something

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

Hi Thomas, On 10/25/2015 01:06 PM, Thomas Girke wrote: I fixed this in systemPipeR versions 1.4.3/1.5.3. The reason for this error was that the tx_type column contains only NA values when a txdb is generated with makeTxDbFromUCSC(). Returning here something more meaningful may be useful, such

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

Hi Hervé and Sonali, Thanks for looking into this option. Your suggestion makes a lot of sense. In general, I find it very useful to know what types of transcripts/genes are included (or missing) in GRanges/GRangesList instances obtained from txdb objects. For this, the tx_type classification is