While this was working in the past, I can't produce a Gene Region Track from my txdb object anymore.
I produce a txdb with:
txdb <- makeTxDbFromGFF("/mnt/Prairie_Vole_Data/Arjen_Folder/Arjen/genomefiles_mo/NCBI/GCF_000317375.1_MicOch1.0_genomic.gff")
wbich results in some warnings:
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: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0$ID, : some transcripts have no "transcript_id" attribute ==> their name ("tx_name" column in the TxDb object) was set to NA 2: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0$ID, : the transcript names ("tx_name" column in the TxDb object) imported from the "transcript_id" attribute are not unique 3: In .find_exon_cds(exons, cds) : The following transcripts have exons that contain more than one CDS (only the first CDS was kept for each exon): rna-NM_001289870.1, rna-NM_001290102.1, rna-NM_001290499.1, rna-NM_001291243.1
I don't think those errors were a problem in the past, but unsure about that. In any case, when I try to
Gene_track <- GeneRegionTrack(txdb, chromosome = "NW_004949099.1", start = 2632436, end = 26371904, options(ucscChromosomeNames=FALSE))
I get this back:
Error in `rownames<-`(`*tmp*`, value = names(x)) : missing values not allowed in rownamesenter code here
I did update Gviz and GenomicFeatures after this problem appeared, but that did not help. Advice is would be highly appreciated!