swaruplabUCI/ArchRtoSignac

Frangments dir with version 1.0.3

Opened this issue · 11 comments

A-legac45 commented

Hello I am also troubling with the fragment files which are the output of cellranger 10x multiomic data

seurat_atac <- ArchR2Signac(

ArchRProject = project_Peaks_MACS2_RES0.9,
refversion = "mm10",
#samples = samplelist, # list of samples in the ArchRProject (default will use ArchRProject@cellColData$Sample but another list can be provided)
fragments_dir = inputFiles,
pm = pkm, # peak matrix from getPeakMatrix(),
fragments_file_extension = '_fragments.tsv.gz',
fragments_fromcellranger = "YES", # fragments_fromcellranger This is an Yes or No selection ("NO" | "N" | "No" or "YES" | "Y" | "Yes")
annotation = annotation # annotation from getAnnotation()
)
[1] "In Progress:"
[1] "Prepare Seurat list for each sample"
[1] "First_try_multiomic_archr"
[1] 121983 3733
Error in CreateFragmentObject(path = fragments, cells = cells, validate.fragments = validate.fragments, :
Fragment file does not exist.

For InputFiles I try many things
InputFiles <- c("/Users/alegac/Library/CloudStorage/OneDrive-INSTITUTCURIE/Projet_linda_mutiomic_novembre/KDI_2017426_2023-11-15_16-59-39/")
InputFiles <- c("/Users/alegac/Library/CloudStorage/OneDrive-INSTITUTCURIE/Projet_linda_mutiomic_novembre/KDI_2017426_2023-11-15_16-59-39")
InputFiles <- c("/Users/alegac/Library/CloudStorage/OneDrive-INSTITUTCURIE/Projet_linda_mutiomic_novembre/KDI_2017426_2023-11-15_16-59-39/atac_fragments.tsv.gz")

Thanks for help

rootze commented

Hello @A-legac45, Thanks for using ArchRtoSignac package

Before everything, do you only have one sample? If so, please update your ArchRtoSignac package; I recently encountered some requests with working on only one sample, so made a minor update in the ArchRtoSignac package, hope it works. BE CAUTIOUS when you update the ArchRtoSignac package, please don't update anything else; recent updates of the Seurat and SeuratObject packages may change something for other packages supporting Seurat V4.

Maybe try this from ****STEP 3 Option2:

fragments_dirs <- c(
"/Users/alegac/Library/CloudStorage/OneDrive-INSTITUTCURIE/Projet_linda_mutiomic_novembre/KDI_2017426_2023-11-15_16-59-39/atac_"
)

# Call the ArchR2Signac function with the provided arguments
seurat_atac <- ArchR2Signac(
  ArchRProject = project_Peaks_MACS2_RES0.9,
  refversion = "mm10",
  fragments_dir = fragments_dirs,
  pm = pkm,
  fragments_fromcellranger = "NO",
  fragments_file_extension = 'fragments.tsv.gz', # instead of using fragments_file_extension (.tsv.gz or .fragments.tsv.gz), here just use the whole name fragments.tsv.gz
  annotation = annotations
)

I see the fragments_fromcellranger parameter is a bit confusing when choosing NO,
fragments_fromcellranger = 'NO' is for fragments from NON Cellranger ATAC output or even from Cellranger ATAC output but don't match the standard output PATH from Cellranger ATAC cellranger-atac count

Please let me know if it works or not, more than happy to help you more.

A-legac45 commented

Hello I have only one sample. Multiomic 10x dataset

I try this but still not working :

fragments_dirs <- c(

  • "/Users/alegac/Documents/archr_linda_multiom_dec_2023/"
  • )

or

fragments_dirs <- c(
"/Users/alegac/Documents/archr_linda_multiom_dec_2023/atac_"
)

seurat_atac <- ArchR2Signac(

  • ArchRProject = project_Peaks_MACS2_RES0.5,
  • refversion = "mm10",
  • fragments_dir = fragments_dirs,
  • pm = pkm,
  • fragments_fromcellranger = "YES",
  • fragments_file_extension = 'atac_fragments.tsv.gz', # instead of using fragments_file_extension (.tsv.gz or .fragments.tsv.gz), here just use the whole name fragments.tsv.gz
  • annotation = annotation
  • )
    [1] "In Progress:"
    [1] "Prepare Seurat list for each sample"
    [1] "First_try_multiomic_archr"
    [1] 121983 3733
    Error in CreateFragmentObject(path = fragments, cells = cells, validate.fragments = validate.fragments, :
    Fragment file does not exist.
A-legac45 commented
A-legac45 commented
rootze commented

Hello @A-legac45,

I cannot see your attached screenshots. I don't think GitHub supports that with email replies.
However, please double-check what I provided for you in my last reply. I made changes not only to fragments_dirs but also fragments_fromcellranger and fragments_file_extension

# Once again here is the code that I changed for you earlier 
fragments_dirs <- c(
"/Users/alegac/Library/CloudStorage/OneDrive-INSTITUTCURIE/Projet_linda_mutiomic_novembre/KDI_2017426_2023-11-15_16-59-39/atac_"
)

# Call the ArchR2Signac function with the provided arguments
seurat_atac <- ArchR2Signac(
  ArchRProject = project_Peaks_MACS2_RES0.9,
  refversion = "mm10",
  fragments_dir = fragments_dirs,
  pm = pkm,
  fragments_fromcellranger = "NO",
  fragments_file_extension = 'fragments.tsv.gz', # instead of using fragments_file_extension (.tsv.gz or .fragments.tsv.gz), here just use the whole name fragments.tsv.gz
  annotation = annotations
)

BUT What you had is

seurat_atac <- ArchR2Signac(
      ArchRProject = project_Peaks_MACS2_RES0.5,
       refversion = "mm10",
       fragments_dir = fragments_dirs,
       pm = pkm,
  *   fragments_fromcellranger = "YES",
  *   fragments_file_extension = 'atac_fragments.tsv.gz', # instead of using fragments_file_extension (.tsv.gz or .fragments.tsv.gz), here just use the whole name fragments.tsv.gz
       annotation = annotation
      )
A-legac45 commented
rootze commented

fragments_dirs <- c(

  • "/Users/alegac/Documents/archr_linda_multiom_dec_2023/atac_" + )

@A-legac45 It seems to me that your fragment PATH has changed. Can you show me what your PATH to the files and what files are inside that folder?

A-legac45 commented
A-legac45 commented
rootze commented

The achr projet is filtered may be this is were the problem come from?

Hello @A-legac45,

It could be. I am not sure. I have very limited experience with true multi-omic datasets. Are you using a public dataset?

mitchTwoTimes commented

Hi @A-legac45 and @rootze,

If this is still an issue I think I was able to get it to work by going in to the ArchR2Signac function and changing a few things to match the cell ranger ARC output.

Line 12:
output_dir = "/croo_output/"

Lines 15/16 :

cur_fragments <- ifelse(is.list(fragments_dir), paste0(fragments_dir[[which(samples == 
                                                                                    cur_sample)]], output_dir, "atac_fragments.tsv.gz"),