Error in dmDSdata

[xpli2020]

Hi,

We are using pipeline from nanopore: Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads and we got stuck on the step with DRIMSeq on our own data (
using Arabidopsis genome annotation file TAIR10_GFF3_genes.gff and TAIR10_cdna_20101212_updated.fna). I think the problem comes from de_analysis.R script and pointing to txdf$TXNAME with version numbers and rownames(cts) the version numbers were removed. Therefore, none would be matched to input into dmDSdata(). Maybe you guys can look into it more.

Thanks,

Warning message:
package ‘DRIMSeq’ was built under R version 4.0.3
Warning messages:
1: package ‘GenomicFeatures’ was built under R version 4.0.3
2: package ‘S4Vectors’ was built under R version 4.0.3
3: package ‘IRanges’ was built under R version 4.0.3
4: package ‘GenomeInfoDb’ was built under R version 4.0.3
5: package ‘GenomicRanges’ was built under R version 4.0.3
6: package ‘AnnotationDbi’ was built under R version 4.0.3
7: package ‘Biobase’ was built under R version 4.0.3
Loading counts, conditions and parameters.
Loading annotation database.
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_exons_from_GRanges(exon_IDX, gr, mcols0, tx_IDX, feature = "exon", :
6277 exons couldn't be linked to a transcript so were dropped (showing
only the first 6):
seqid start end strand ID Name Parent Parent_type
1 Chr1 433031 433819 - AT1G02228.1
2 Chr1 846664 847739 + AT1G03420.1
3 Chr1 2070737 2070893 + AT1G06740.1
4 Chr1 2071102 2073535 + AT1G06740.1
5 Chr1 2415041 2415970 + AT1G07800.1
6 Chr1 2531695 2534786 - AT1G08105.1
2: In .extract_exons_from_GRanges(cds_IDX, gr, mcols0, tx_IDX, feature = "cds", :
197160 CDS couldn't be linked to a transcript so were dropped (showing
only the first 6):
seqid start end strand ID Name Parent Parent_type
1 Chr1 3760 3913 + AT1G01010.1-Protein
2 Chr1 3996 4276 + AT1G01010.1-Protein
3 Chr1 4486 4605 + AT1G01010.1-Protein
4 Chr1 4706 5095 + AT1G01010.1-Protein
5 Chr1 5174 5326 + AT1G01010.1-Protein
6 Chr1 5439 5630 + AT1G01010.1-Protein
'select()' returned 1:many mapping between keys and columns
Filtering counts using DRIMSeq.
Error in dmDSdata(counts = counts, samples = coldata) :
mode(counts) %in% "numeric" is not TRUE
Calls: dmDSdata -> stopifnot
Execution halted
[Tue Mar 9 15:27:59 2021]