greenleaflab/10x-scatac-2019

Publication Page for Satpathy*, Granja* et al 2019

10x-scatac-2019's Issues

TF footprinting script

Hi,
Thanks for sharing the code.

But I couldn't find code about 'TF footprinting analysis' from the available scripts. Since I couldn't tell some detail about this part just from paper, I would really appreciate it if you are willing to share with us.

Best,
Huan

Using this repository for CNV Analysis

Hi, I'm an ArchR user that was directed to this repository to perform CNV Analysis since the feature is not yet available in ArchR.

I have a few questions about how this repository works. I see that the work is transferred from step to step via RDS files, so since CNV analysis is the 8th step, I will have to do some number of steps before. Which are necessary?

Another question I have is how to input multiple fragment files. I noticed that a list of vector paths, like in ArchR, doesn't work on the first step, though a single file path does. Is there a way to do this with multiple files?

Thanks!

Hugo Kitano

Analyze the umap trajectory

Hi,
Thanks for your great works and sharing your code. When I use your analyze the umap trajectory code to construct the trajectory in my own data, I have some questions. Hope you can help me figure out.
I feel a little confused that if I have no idea the development background in my data, how can I choose the clusters to build the trajectory? In the paper, you extract the B cell associated cluster to reverse reconstruction of B cell differentiation trajectory. I wanna know can I use the unsupervised methods to learn the trajectory.
Some specific questions for your code, how you choose the latest cluster? And which matrix contain the delta ATAC number between each cluster?
Thanks a lot.

..

fragments <- fragments[mcols(fragments)[,by] %in% rownames(tssSingles)[tssSingles$cellCall==1]]
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘NSBS’ for signature ‘"standardGeneric"’

Request the human-mouse hybrid analysis gene.ranges and tss.ranges settings

Hi,

I am rerunning your human-mouse cell mixture data, but I cannot find a proper list to use for gene.ranges and tss.ranges. Could you share with me how you find a proper list for the human and mouse genes when you analysis by Signac?

Thank you so much!

Z

Plot CNA

Good day!

I am currently using ArchR. Great package! However, there is no implementation of CNA there (maybe in the future?). I have generated the cnaObj based on the code you shared. However, I am not sure how to plot the results. Could you please share how to do it and generate a nice figure like the one in your publication?

Thanks in advance!

would you consider providing an example of analysis using 10x's output

data on NCBI not downloadable

Hi,

I am trying to access some public data from your paper and I followed the instructions of "Getting 10x scATAC-seq Bam Files" in README. In the final figure of README, the bam file link is downloadable but as you can see below there isn't any downloadable link for the bam file. I also tried to get bam files using AWS but it didn't work.

I only need to have access to the following bam files;

• Dendritic cells
• CD4 Memory T cells
• CD4 Naïve T cells
• Bone Marrow
• CD34 Progenitors

If you can point me to the files or guide me how to get them, I'll really appreciate.

Many thanks,
Ravza

05_Cluster_Unique_Peaks_v2.R - changes needed for identifying unique gene activities

Was just wondering if someone might be able to comment on what changes would be needed to adapt the 05_Cluster_Unique_Peaks_v2.R script to make it appropriate for detecting unique gene activities, rather than using peaks.

From a review of the script and the methods section of the manuscript, it seems like at changing the 1st argument of the uniqueFeatures() function from:
edgeR::cpm(assay(sePB),log=TRUE,prior.count=3)
to
log2(edgeR::cpm(2^assay(sePB)-1) +1) would be required.

Similarly, it seemed like it may be necessary to change the lines 144, 175, 185, 254, and 263 in the createPseudoBulk() function, to first convert back to gene activity scores and then log transform, however I wasn't sure about that.

Would be great to hear anyones thoughts on those changes and any others that might be required to work with gene activities rather than peaks.

Thanks in advance!

Ask for Cicero PBMC dataset

Do you have the file just like this ? This is the Cicero hematopoiesis datasets from your work. The author of paper "Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity" said that we can obtain Cicero PBMC dataset by contacting to you. Look forward your reply!

unable to find an inherited method for function ‘NSBS’ for signature ‘"standardGeneric"’

Hello,
It's really an awsome wroking. But I got a error by using your workflow in 01_Filter_Cells_v2, as following:

fragments <- fragments[mcols(fragments)[,by] %in% rownames(tssSingles)[tssSingles$cellCall==1]]
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘NSBS’ for signature ‘"standardGeneric"’

I don't know the ### mcols(fragments)[,by] meaning, and I got error in this formula.
Hope you could help me out.

Thanks

NO fragments.tsv.gz OF Hematopoiesis cells

Hi,
I have downloaded scATAC_Heme_All_SummarizedExperiment.final.rds followed your links.
I checked the Group information in colData. And I also want to use the segments files from this cells.

table(Heme_meta_info$Group)

                B_Cells                  BM_pDC        Bone_Marrow_Rep1
                   2982                     162                    6011
  CD34_Progenitors_Rep1   CD34_Progenitors_Rep2             CD4_HelperT
                  10056                    4764                    1413
                    CLP                     CMP         Dendritic_Cells
                     92                     585                    1265
                    GMP                     HSC                    LMPP
                    471                     349                      90
Memory_CD4_T_Cells_Rep1 Memory_CD4_T_Cells_Rep2      Memory_CD8_T_Cells
                   1206                    1416                    1089
                    MEP               Monocytes                     MPP
                    181                    1868                     146
 Naive_CD4_T_Cells_Rep1  Naive_CD4_T_Cells_Rep2       Naive_CD8_T_Cells
                    625                    1888                    1945
               NK_Cells               PBMC_Rep1               PBMC_Rep2
                   1110                    9616                    6163
              PBMC_Rep3               PBMC_Rep4      Regulatory_T_Cells
                   4847                     944                    2598

I could find most of them from GSE129785_RAW.tar in GSE129785.
But I also need segmants files of CLP, CMP, GMP, HSC, LMPP, MEP and MPP
which I guessed from your CELL PAPER Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation. But there weren't paired segmants submiited in GSE96769.
Can you re-submitted segments files of the Hematopoiesis cells on GEO datasets again or other ways?
Thanks a lot.

02

Making Seurat LSI Object...
Binarizing matrix...
Getting top 20000 features...
Computing Term Frequency IDF...
Computing SVD using irlba...
Making Seurat Object...
Error in CreateSeuratObject(mat, project = "scATAC", min.cells = 0, min.genes = 0) :
unused argument (min.genes = 0)

Unable to fine the dataset of PICS_GWAS_SNPS.gr.rds

Hi,

I really appreciate your work on scATAC-seq.

I tried to run GWAS chromVAR on single-cell summarized experiment using co-accessibility. However, I was unable to find the dataset of PICS_GWAS_SNPS.gr.rds.

Would it be possible to provide this data?

Thank you so much!

Cannot find original bam file on NCBI

Hi,
I am trying to get the public data of your paper and I followed the instructions of "Getting 10x scATAC-seq Bam Files" in README. However I failed to find bam files in original format, which is mentioned in the last step.


Could you let me know where to find these files? Thanks a lot!

data availability

Thank you very much for the inspiring publication. We are wondering if it'd be possible that you can share cluster identity, cell barcode and peak count matrix corresponding to the Fig 5a. In your shared data it seems to be lacking them. It would be very much appreciated.

Best,
Rong