gravatar for David_emir

2 hours ago by


Hi All,

We did Single Cell RNA data analysis from 25 diseased patients. The Vendor sent 25.MTX files to us. The files we received is as follows

├── barcodes.tsv.gz
├── features.tsv.gz
└── matrix.mtx.gz
0 directories, 3 files

The data comes off the machine as bcl files and is converted to counted matrix files using 'cellranger mkfastq' and 'cellrangercount.
My question is we have 25 different.mtx.gz files and we sequenced ~ 2000 cells/Sample.

  1. Should we merge these 25.mtx.gz files to create ONE new Master Matrix file for further analysis? like Columns(2000*25) of cell barcodes and 32000 rows of gene name into one super Master file. like how we used to do in Bulk RNA seq data analysis.
  2. Whats the best way to annotate Gene names?
  3. Please let me know the best pipeline for scRNA data analysis - we are biologists with limited experience in coding.

Thanks a lot for helping us,
Have a great day ahead.



modified 2 hours ago

2 hours ago


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