Question: Problem with finding mitochondrial genes in a human single cell RNA-Seq readCounts file
0
gravatar for es.azadian
4 months 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 4 months ago by Aaron Lun22k • written 4 months ago by es.azadian0
Answer: Problem with finding mitochondrial genes in a human single cell RNA-Seq readCoun
1
gravatar for Aaron Lun
4 months ago by
Aaron Lun22k
Cambridge, United Kingdom
Aaron Lun22k 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 4 months ago • written 4 months ago by Aaron Lun22k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 184 users visited in the last hour