Problem with finding mitochondrial genes in a human single cell RNA-Seq readCounts file
1
0
Entering edit mode
es.azadian • 0
@esazadian-17093
Last seen 3.0 years ago

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.

single-cell rnaseq mitochondria • 490 views
ADD COMMENT
1
Entering edit mode
Aaron Lun ★ 27k
@alun
Last seen 13 hours ago
The city by the bay
  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 COMMENT

Login before adding your answer.

Traffic: 437 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6