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I removed chromosomes that are reported to be detected 0 Fragments according to the log file by adding excludeChr = chromosome_ids when creating ARROW file. I still encountered ERROR:
<simpleError in .getFragsFromArrow(ArrowFile = ArrowFile, chr = names(featureList)[x], out = "IRanges", cellNames = cellNames): Chromosome NA not in ArrowFile! Available Chromosomes are : NC_013276.1,NW_024429180.1,NW_024429181.1,NW_024429182.1,...
Below are the code that I used to create gene annotation: genomeAnnotation <- createGenomeAnnotation(genome = Bsgenome.BCM.Maur2.0, filter=FALSE) txdb <- TxDb.Mesocricetus.auratus.v1 genes <- genes(txdb) tss <- promoters(genes, upstream = 0, downstream = 1) exons <- exons(txdb) geneAnnotation <- createGeneAnnotation( TSS = tss, exons = exons, genes = genes )
Below are the code that I used to create ARROW files: ArrowFiles <- createArrowFiles( inputFiles = inputFiles, sampleNames = names(inputFiles), minTSS = 4, minFrags = 1000, addTileMat = TRUE, addGeneScoreMat = TRUE, genomeAnnotation = genomeAnnotation, geneAnnotation = geneAnnotation, subThreading = FALSE, excludeChr = chromosome_ids )
What should I do next to create the ARROW files?
The text was updated successfully, but these errors were encountered:
Hi @YaoyJiang! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other
responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire
a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know!
In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15.
Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.
My log file:
ArchR-createArrows-2a3c284c353742-Date-2024-04-15_Time-01-37-40.623548.log
I removed chromosomes that are reported to be detected 0 Fragments according to the log file by adding
excludeChr = chromosome_ids
when creating ARROW file. I still encountered ERROR:<simpleError in .getFragsFromArrow(ArrowFile = ArrowFile, chr = names(featureList)[x], out = "IRanges", cellNames = cellNames): Chromosome NA not in ArrowFile! Available Chromosomes are : NC_013276.1,NW_024429180.1,NW_024429181.1,NW_024429182.1,...
Below are the code that I used to create gene annotation:
genomeAnnotation <- createGenomeAnnotation(genome = Bsgenome.BCM.Maur2.0, filter=FALSE) txdb <- TxDb.Mesocricetus.auratus.v1 genes <- genes(txdb) tss <- promoters(genes, upstream = 0, downstream = 1) exons <- exons(txdb) geneAnnotation <- createGeneAnnotation( TSS = tss, exons = exons, genes = genes )
Below are the code that I used to create ARROW files:
ArrowFiles <- createArrowFiles( inputFiles = inputFiles, sampleNames = names(inputFiles), minTSS = 4, minFrags = 1000, addTileMat = TRUE, addGeneScoreMat = TRUE, genomeAnnotation = genomeAnnotation, geneAnnotation = geneAnnotation, subThreading = FALSE, excludeChr = chromosome_ids )
What should I do next to create the ARROW files?
The text was updated successfully, but these errors were encountered: