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Question: Problem with finding mitochondrial genes in a human single cell RNA-Seq readCounts file
0
gravatar for es.azadian
11 weeks ago by
es.azadian0
es.azadian0 wrote:

I am trying to find a way to conveniently recognize mitochondrial genes in a csv file, which is a readcounts for single-seq RNA-Seq data obtaiened from human.

The workflow that I’m working with (https://f1000research.com/articles/5-2122/v2) has used the following command:

is.mito <- grepl("^mt-", rownames(sce))

When I run this command I do not face any error, but then there is nothing in is.mito. Following is a schematic of this csv file:  

                                   BR21_1_SC1_052113      BR21_1_SC2_052113      BR21_1_SC3_052113

eg:1:chr19:m                           0                                         0                                       0

eg:10:chr8:p                            0                                        145                                    0

eg:100:chr20:m                       29                                        0                                     18

 

 

Thanks for your help.

ADD COMMENTlink modified 10 weeks ago by Aaron Lun21k • written 11 weeks ago by es.azadian0
1
gravatar for Aaron Lun
10 weeks ago by
Aaron Lun21k
Cambridge, United Kingdom
Aaron Lun21k wrote:
  1. Please tag questions with the name of the workflow, simpleSingleCell.
  2. Your rows are obviously named under a different scheme from the data set used in the workflow. I would guess that the first number is the Entrez gene ID, the following field is the chromosome, and I don't know what the last field is. I don't know why you have such a complicated naming structure, but it should be clear that mitochondrial genes will not start with mt, but will instead be identified by chrM.
  3. I really hope you have more than three cells. Some steps will simply fail with such a small data set.
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Aaron Lun21k
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