Open A-legac45 opened 11 months ago
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.
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_dec2023/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.
Hello I have only one sample. Multiomic 10x dataset
I try this but still not working :
fragments_dirs <- c(
or
fragments_dirs <- c( "/Users/alegac/Documents/archr_linda_multiom_dec2023/atac" )
seurat_atac <- ArchR2Signac(
here you will find the structure of my folder "/Users/alegac/Documents/archr_linda_multiom_dec_2023/
De : Ze @.> Envoyé : jeudi 21 décembre 2023 21:41 À : swaruplabUCI/ArchRtoSignac @.> Cc : Le Gac Anne-Laure @.>; Mention @.> Objet : Re: [swaruplabUCI/ArchRtoSignac] Frangments dir with version 1.0.3 (Issue #33)
Hello @A-legac45https://github.com/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_2023-11-1516-59-39/atac" )
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.
— Reply to this email directly, view it on GitHubhttps://github.com/swaruplabUCI/ArchRtoSignac/issues/33#issuecomment-1866903876, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AYDTLNX4MYSIEOWCAQBFKDTYKSNGVAVCNFSM6AAAAABA6LDDH2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRWHEYDGOBXGY. You are receiving this because you were mentioned.Message ID: @.***>
fragments <- CreateFragmentObject(path = fragments_dirs, cells = Cells(pkm), validate.fragments = TRUE) Computing hash Checking for 3733 cell barcodes Error in CreateFragmentObject(path = fragments_dirs, cells = Cells(pkm), : Not all cells requested could be found in the fragment file. fragments <- CreateFragmentObject(path = fragments_dirs, cells = Cells(pkm), validate.fragments = F) Computing hash all(colnames(pkm) %in% Cells(fragments)) [1] TRUE
De : Le Gac Anne-Laure @.> Envoyé : jeudi 21 décembre 2023 22:54 À : swaruplabUCI/ArchRtoSignac @.> Objet : RE: [swaruplabUCI/ArchRtoSignac] Frangments dir with version 1.0.3 (Issue #33)
Hello I have only one sample. Multiomic 10x dataset
I try this but still not working :
fragments_dirs <- c(
or
fragments_dirs <- c( "/Users/alegac/Documents/archr_linda_multiom_dec2023/atac" )
seurat_atac <- ArchR2Signac(
here you will find the structure of my folder "/Users/alegac/Documents/archr_linda_multiom_dec_2023/
De : Ze @.> Envoyé : jeudi 21 décembre 2023 21:41 À : swaruplabUCI/ArchRtoSignac @.> Cc : Le Gac Anne-Laure @.>; Mention @.> Objet : Re: [swaruplabUCI/ArchRtoSignac] Frangments dir with version 1.0.3 (Issue #33)
Hello @A-legac45https://github.com/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_2023-11-1516-59-39/atac" )
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.
— Reply to this email directly, view it on GitHubhttps://github.com/swaruplabUCI/ArchRtoSignac/issues/33#issuecomment-1866903876, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AYDTLNX4MYSIEOWCAQBFKDTYKSNGVAVCNFSM6AAAAABA6LDDH2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRWHEYDGOBXGY. You are receiving this because you were mentioned.Message ID: @.***>
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
)
It still not working
fragments_dirs <- c(
- "/Users/alegac/Documents/archr_linda_multiom_dec2023/atac"
- ) seurat_atac <- ArchR2Signac(
- ArchRProject = project_Peaks_MACS2_RES0.5,
- 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 = annotation
- ) [1] "IF selecting NO, please make sure to provide fragments_file_extension" [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.
Do you want me too send you my archr project or my fragment files??
De : Ze @.> Envoyé : jeudi 21 décembre 2023 23:08 À : swaruplabUCI/ArchRtoSignac @.> Cc : Le Gac Anne-Laure @.>; Mention @.> Objet : Re: [swaruplabUCI/ArchRtoSignac] Frangments dir with version 1.0.3 (Issue #33)
Hello @A-legac45https://github.com/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 changed not only to fragments_dirs but also fragments_fromcellranger and fragments_file_extension
fragments_dirs <- c( "/Users/alegac/Library/CloudStorage/OneDrive-INSTITUTCURIE/Projet_linda_mutiomic_novembre/KDI_2017426_2023-11-1516-59-39/atac" )
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,
— Reply to this email directly, view it on GitHubhttps://github.com/swaruplabUCI/ArchRtoSignac/issues/33#issuecomment-1866991802, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AYDTLNU37RQDSDUEVGSS5J3YKSXPRAVCNFSM6AAAAABA6LDDH2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRWHE4TCOBQGI. You are receiving this because you were mentioned.Message ID: @.***>
fragments_dirs <- c(
- "/Users/alegac/Documents/archr_linda_multiom_dec2023/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?
I try this :
fragments_dirs <- c("/Users/alegac/Documents/archr_linda_multiom_dec2023/atac")
seurat_atac <- ArchR2Signac( ArchRProject = project_Peaks_MACS2_RES0.5, refversion = "BSgenome.Mmusculus.UCSC.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 = annotation )
[1] "IF selecting NO, please make sure to provide fragments_file_extension" [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.
the folder contain the following files [cid:a1ac8f48-3f18-4a3a-9167-039b6bd8f9b2]
De : Ze @.> Envoyé : vendredi 22 décembre 2023 00:26 À : swaruplabUCI/ArchRtoSignac @.> Cc : Le Gac Anne-Laure @.>; Mention @.> Objet : Re: [swaruplabUCI/ArchRtoSignac] Frangments dir with version 1.0.3 (Issue #33)
fragments_dirs <- c(
@A-legac45https://github.com/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?
— Reply to this email directly, view it on GitHubhttps://github.com/swaruplabUCI/ArchRtoSignac/issues/33#issuecomment-1867047655, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AYDTLNRXENRH26L3ZHLJULDYKTATLAVCNFSM6AAAAABA6LDDH2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRXGA2DONRVGU. You are receiving this because you were mentioned.Message ID: @.***>
Hello Ze,
I have tried this also I do not know if this can help :
fragments_dirs <- c("/Users/alegac/Documents/archr_linda_multiom_dec_2023/atac_fragments.tsv.gz") fragments <- CreateFragmentObject(path = fragments_dirs, cells = Cells(pkm), validate.fragments = F) Computing hash
all(colnames(pkm) %in% Cells(fragments)) [1] TRUE
fragments <- CreateFragmentObject(path = fragments_dirs, cells = Cells(pkm), validate.fragments = T) Computing hash Checking for 3733 cell barcodes Error in CreateFragmentObject(path = fragments_dirs, cells = Cells(pkm), : Not all cells requested could be found in the fragment file.
The achr projet is filtered may be this is were the problem come from?
De : Le Gac Anne-Laure @.> Envoyé : vendredi 22 décembre 2023 10:26 À : swaruplabUCI/ArchRtoSignac @.> Objet : RE: [swaruplabUCI/ArchRtoSignac] Frangments dir with version 1.0.3 (Issue #33)
I try this :
fragments_dirs <- c("/Users/alegac/Documents/archr_linda_multiom_dec2023/atac")
seurat_atac <- ArchR2Signac( ArchRProject = project_Peaks_MACS2_RES0.5, refversion = "BSgenome.Mmusculus.UCSC.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 = annotation )
[1] "IF selecting NO, please make sure to provide fragments_file_extension" [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.
the folder contain the following files [cid:a1ac8f48-3f18-4a3a-9167-039b6bd8f9b2]
De : Ze @.> Envoyé : vendredi 22 décembre 2023 00:26 À : swaruplabUCI/ArchRtoSignac @.> Cc : Le Gac Anne-Laure @.>; Mention @.> Objet : Re: [swaruplabUCI/ArchRtoSignac] Frangments dir with version 1.0.3 (Issue #33)
fragments_dirs <- c(
@A-legac45https://github.com/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?
— Reply to this email directly, view it on GitHubhttps://github.com/swaruplabUCI/ArchRtoSignac/issues/33#issuecomment-1867047655, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AYDTLNRXENRH26L3ZHLJULDYKTATLAVCNFSM6AAAAABA6LDDH2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRXGA2DONRVGU. You are receiving this because you were mentioned.Message ID: @.***>
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?
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"),
Hello I am also troubling with the fragment files which are the output of cellranger 10x multiomic data
seurat_atac <- ArchR2Signac(
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