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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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Creating ARROW files :ERROR Found in .fastTSSCounts for (Mock1 : 1 of 1) #2149

Open YaoyJiang opened 4 months ago

YaoyJiang commented 4 months ago

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?

rcorces commented 4 months ago

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.

rersister commented 4 months ago

@YaoyJiang Hello, how about this question, I am facing this problem same as you. Is there any suggestion to solve it. Thanks a lot.