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Since genes, transcripts and exons are fetched independently in makeTxDbFromBiomart, there should be a check for zero exon genes. This could happen when BioMart queries silently (no error) skip exons. Here's a example BioMart query that skips exons.
[http://aug2017.archive.ensembl.org/biomart/martservice?query=<Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" ><Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_transcript_id'/><Attribute name = 'rank'/><Attribute name = 'exon_chrom_start'/><Attribute name = 'ensembl_exon_id'/><Attribute name = 'genomic_coding_start'/><Attribute name = 'genomic_coding_end'/><Attribute name = '5_utr_start'/><Attribute name = '5_utr_end'/><Attribute name = '3_utr_start'/><Attribute name = '3_utr_end'/><Attribute name = 'cds_start'/><Attribute name = 'cds_end'/><Attribute name = 'cds_length'/><Filter name = 'transcript_gencode_basic' excluded = "0" /><Filter name = 'chromosome_name' value = '1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT' /></Query>]
The text was updated successfully, but these errors were encountered:
hpages
transferred this issue from Bioconductor/GenomicFeatures
Mar 23, 2024
Since genes, transcripts and exons are fetched independently in makeTxDbFromBiomart, there should be a check for zero exon genes. This could happen when BioMart queries silently (no error) skip exons. Here's a example BioMart query that skips exons.
[http://aug2017.archive.ensembl.org/biomart/martservice?query=<Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" ><Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_transcript_id'/><Attribute name = 'rank'/><Attribute name = 'exon_chrom_start'/><Attribute name = 'ensembl_exon_id'/><Attribute name = 'genomic_coding_start'/><Attribute name = 'genomic_coding_end'/><Attribute name = '5_utr_start'/><Attribute name = '5_utr_end'/><Attribute name = '3_utr_start'/><Attribute name = '3_utr_end'/><Attribute name = 'cds_start'/><Attribute name = 'cds_end'/><Attribute name = 'cds_length'/><Filter name = 'transcript_gencode_basic' excluded = "0" /><Filter name = 'chromosome_name' value = '1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT' /></Query>]
The text was updated successfully, but these errors were encountered: