Question: integrate eight single cell *.csv files into one *.csv file
0
gravatar for yueli7
6 weeks ago by
yueli7140
China
yueli7140 wrote:

Hello,

I have eight single cell *.csv files and want to integrate them into one *.csv file Then I can do the downstream Seurat analysis: https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html.

How can I do it?

Thanks in advance for great help!

Best,

Yue

rna-seq • 119 views
ADD COMMENTlink modified 6 weeks ago by Mensur Dlakic5.8k • written 6 weeks ago by yueli7140
1

This will work only if all files have the same number of rows:

paste -d"," file1 file2 file3 file4 file5 file6 file7 file8 > all_together.csv
ADD REPLYlink written 6 weeks ago by Mensur Dlakic5.8k

Hello Mensur Dlakic,

Thank yo so much for your great help!

You are right!

Best,

Yue

ADD REPLYlink written 5 weeks ago by yueli7140

It depends on what these files are. Are those counts? And if so do they come from different experiments and are they normalized, and if so how? Please add some details.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by ATpoint36k

Hello ATpoint,

Thank you so much for your response!

I downloaded the files from: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122960.

These files ended with: *_filtered_gene_bc_matrices_h5.h5.

I used cellranger mat2csv to transfer eight files into csv format.

Right now, I want to merge them together,

How I can do it?

Thank you again for your great help!

Best,

Yue

li@li-:~/cellranger-3.1.0/cellranger-cs/3.1.0/bin$ ./cellranger mat2csv /home/li/donor/GSM3489185_Donor_01_filtered_gene_bc_matrices_h5.h5 85.csv
ADD REPLYlink written 6 weeks ago by yueli7140
1

So this looks like eight different donors with raw data in H5 format. No need to bring them from the compressed format to plain text. I'd probably use Read10X_h5 from Seurat to directly import them into R. Then first perform a QC using the standard Seurat workflow on each of the samples. Once you have your final matrix of high-quality cells per sample you can go and integrate them, e.g. with the Seurat anchoring framework as described on their website. Check the vignettes on how to combine different samples in Seurat, I cannot help with this since I personally use Bioconductor packages for scRNA-seq, not Seurat.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by ATpoint36k
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