Question: warning in makeTxDbFromGFF
0
gravatar for layal8785
2.5 years ago by
layal87850
layal87850 wrote:

The warning in creating TxDb:

gtffile <- file.path("PATH/Mus_musculus.GRCm38.86.gtf")

txdb <- makeTxDbFromGFF(gtffile, format="gtf")

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning messages:
1: Named parameters not used in query: internal_chrom_id, chrom, length, is_circular
2: Named parameters not used in query: internal_id, name, type, chrom, strand, start, end
3: Named parameters not used in query: internal_id, name, chrom, strand, start, end
4: Named parameters not used in query: internal_id, name, chrom, strand, start, end
5: Named parameters not used in query: internal_tx_id, exon_rank, internal_exon_id, internal_cds_id
6: Named parameters not used in query: gene_id, internal_tx_id 

 

It doesn't change if I add the other arguments as "dbxrefTag= "GeneName" " or "circ_seqs=character()"

of course I insert the correct path, so PATH is the full path where the gtf file exists:

genomicfeatures • 716 views
ADD COMMENTlink modified 2.5 years ago by James W. MacDonald51k • written 2.5 years ago by layal87850
Answer: warning in makeTxDbFromGFF
0
gravatar for James W. MacDonald
2.5 years ago by
United States
James W. MacDonald51k wrote:

Those are just warnings that you can safely ignore. They will go away when we release the new version of GenomicFeatures in April.

ADD COMMENTlink written 2.5 years ago by James W. MacDonald51k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 151 users visited in the last hour