Issue with chromstaR ATACseq, unable to find genome?

Question

[Ronin]

Hi,

I am running an ATACseq experiment with Perca fluviatilis, and am having some issues with chromstaR. I have a few lines of code so far that I pulled from the user guide. In two parts we have:

library(chromstaR) === Step 1: Preparation === Prepare the file paths. Exchange this with your input and output directories. inputfolder <- "C:/Users/Me/Desktop/NEWATAC" outputfolder <- "C:/Users/Me/Desktop/NEWATAC" Define experiment structure, put NA if you don't have controls Modify the experiment table for your data experiment_table <- data.frame( file = c("C:/Users/Me/Desktop/NEWATAC/01_trim.unique.mapped.sorted", "C:/Users/Me/Desktop/NEWATAC/08_trim.unique.mapped.sorted", "C:/Users/Me/Desktop/NEWATAC/25_trim.unique.mapped.sorted"), mark = "ATACseq", # You might use a generic term like ATAC-seq for open chromatin analysis condition = c("Eye", "Spleen", "Eye"),
replicate = c(1, 2, 3), pairedEndReads = TRUE, controlFiles = c( "C:/Users/Me/Desktop/NEWATAC/01_trim.unique.mapped.sorted" ) ) print(experiment_table)

This part above seems to work fine. Here is where my error comes from:

=== Step 2: Run Chromstar === Run ChromstaR Chromstar( inputfolder, experiment.table = experiment_table, outputfolder = outputfolder,
numCPU = 4, binsize = 1000, stepsize = 500, assembly = "C:/Users/Me/Desktop/NEWATAC/GCF_010015445.1_GENO_Pfluv_1.0_genomic.fasta", chromosomes = NULL, mode = 'differential' )

I get the following output message and error:

Setting up parallel execution with 4 threads ... 0.61s ================ Binning the data ================ Obtaining chromosome length information from UCSC ...Error in .get_chrom_info_for_unregistered_UCSC_genome(genome, assembled.molecules.only = assembled.molecules.only, : unknown UCSC genome:
C:/Users/Me/Desktop/NEWATAC/GCF_010015445.1_GENO_Pfluv_1.0_genomic.fasta

So it is saying there is an unknown UCSC genome, and stops working here. I got the genomic file downloaded from: https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/8168/100/GCF_010015445.1_GENO_Pfluv_1.0/

I am sure I am making some stupid mistake(s), and would really appreciate any tips to solve this probably simple issue! Cheers,

[Ram]

Please do not use the how-to tag: it's not for when you have a question on how to do something, it's for when you're creating a post on how to use the forum. I've removed it this time.

Also, there was no need to use both ATAC-seq and ATACseq tags, I've removed the latter.

[Ram]

Please DO NOT use the quote button to add code, it mangles the content. Use the 101010 button instead.

Right now, your code content has been mangled and cannot be fixed. Please edit your post and copy-paste it again, but this time use the proper 101010 option and not the double quote option.