Question

Making scRNA counts file from barcodes, genes and matrix.mtx file

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6.8 years ago

Paragon ▴ 10

Hello!

I have barcodes.tsv, genes.tsv and matrix.mtx files. I want to generate a sample scRNA counts files using R.

Thanks!

RNA-Seq R • 6.2k views

ADD COMMENT • link updated 6.8 years ago by Devon Ryan 105k • written 6.8 years ago by Paragon ▴ 10

score 2 · Answer 1 · 2018-08-16

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6.8 years ago

Devon Ryan 105k

The context of "I used CellRanger from 10X genomics..." would be needed for most people to provide you with actual help...

matrix.mtx is a MatrixMarket file that can be loaded in R with:

library(Matrix)
m = readMM("matrix.mtx")

The columns are the rows in barcodes.tsv (not that it really matters which is which, you can just ignore this file in my opinion) and the row labels are given in genes.tsv (use the first column).

ADD COMMENT • link 6.8 years ago by Devon Ryan 105k

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Additionally, if you know how you will be analyzing the data, you may want to check the instructions for that pipeline. Many single-cell analysis packages now include a function to read 10x matrix and convert it to the most appropriate format for that package.

ADD REPLY • link 6.8 years ago by igor 13k

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Thank you very much.

ADD REPLY • link 6.8 years ago by Paragon ▴ 10

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Thanks! I'm new in R. May I know how I set the row labels from genes.tsv?

ADD REPLY • link 6.8 years ago by Paragon ▴ 10

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please provide the steps you followed to this, I am also new to this. I will be grateful.

ADD REPLY • link 6.1 years ago by saqlain ▴ 90

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help(row.names) and help(read.csv)

ADD REPLY • link 6.1 years ago by Devon Ryan 105k