Hi Thomas,
I downloaded the fasta file from human Transcriptome and then got rid of
the rRNA'S with Biostrings to make a fasta file without the rRNA sequences.
library(Biostrings)
library(ShortRead)
rna <- readDNAStringSet("human.rna.fna")
nr_idx <- grep("NR",names(rna))
rna2 <- rna[-nr_idx,]
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 mo
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 ex
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 a