Answers.Body: <p>From what I known, there is no clear consensus in the field and it depends on the type of cells you are interrogating. </p>
  
  <p>However, if mitoRNA/endogenousRNA ratio does not fit for your purposes, other option is to <strong>check at the total number of genes/transcripts detected</strong> in each cell. In this way, you can filter out cells that have considerable less genes/transcripts detected than the rest since this may be indicative of bad quality cells for any reason (apoptosis, RNA degradation, sequencing itself, etc). For instance, to <strong>put a threshold</strong> of >1000 genes/transcripts in a cell to be considered for further analysis.</p>
  
  <p>Consider also to take a look at the number of mapped reads for each cell, as cells with low mapped reads respect to the rest could be potentially problematic.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-11T07:06:08.680Z
Answers.Text: What does it mean ‘mapped reads’? How is it different from the expression matrix itself?
Answers.UserDisplayName: Nikita Vlasenko
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-11T11:30:45.397Z
Answers.Text: If you are using UMIs, usually I filter out those that are supported by less than 3 reads and some that do not fulfill QC requirements. In this case UMIs and mapped reads does not correspond (although should be very similar). At the end is another way of perform QC of the data but at an earlier stage of the analysis (before counting molecules and assign them to genes).
Answers.UserDisplayName: jxx_fa
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Answers.CreationDate: 2018-01-10T13:44:39.267Z
Answers.LastActivityDate: 2018-01-10T13:53:23.080Z
Answers.LastEditDate: 2018-01-10T13:53:23.080Z
Answers.UserDisplayName: jxx_fa
Body: <p>I am new to data science. I have a dataset of single-cell gene expression from multiple cell types in <em>C. Elegans</em>. The dataset is from the paper <a href="https://www.ncbi.nlm.nih.gov/pubmed/28818938" rel="nofollow noreferrer">Comprehensive single-cell transcriptional profiling of a multicellular organism</a></p>
  
  <p>My main question is, <strong>Which approaches should I use for filtering out bad cells in this case when we have multiple cell types in the dataset?</strong></p>
  
  <p>So far I tried to filter out genes that have too high mitochondrial genes content following the <a href="https://www.bioconductor.org/help/workflows/simpleSingleCell/" rel="nofollow noreferrer">Bioconductor “simpleSingleCell” workflow</a>.</p>
  
  <p>However, the tutorial specifically says that the method of filtering out based on mitochondrial genes most probably will not work when the dataset has multiple cell types:</p>
  
  <blockquote>
    <p>Analyzing all cell types together would unnecessarily inflate the MAD and 
        compromise the removal of low-quality cells, at best; or lead to the 
        entire loss of one cell type, at worst.</p>
  </blockquote>
  
  <p>Any suggestions would be greatly appreciated. </p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-18T10:27:36.597Z
Comments.Text: By filtering out what do you mean: removing the sample from the analysis when there are too many mithocondrial genes or removing the mitochondrial genes ? (This seems important in scRNAseq and I haven't worked with it, so excuse me if it is a naïve question)
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-20T17:02:30.613Z
Comments.Text: removing the bad quality samples
Comments.UserDisplayName: Nikita Vlasenko
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-10T20:35:41.550Z
Comments.Text: Not a standard, but I found this course helpful http://hemberg-lab.github.io/scRNA.seq.course/ . I personally filter cells with too low or too high transcript counts, cells with low count of detected genes, and cells with high spike-in/endogenous RNA ratio. Prior to this pipeline I also filter out ribosomal RNA. Take it with a grain of salt because I'm still experimenting on it. Also, this answer may help https://bioinformatics.stackexchange.com/a/3171/1771
Comments.UserDisplayName: gc5
Tags: <rna-seq><filtering>
Title: Filter out outliers of the scRNA-seq (heterogenous cells)
ThreadText: # Filter out outliers of the scRNA-seq (heterogenous cells)
  
  (Asked by: username_0 on 2017-12-17)
  
  I am new to data science. I have a dataset of single-cell gene expression from multiple cell types in *C. Elegans*. The dataset is from the paper [Comprehensive single-cell transcriptional profiling of a multicellular organism](https://www.ncbi.nlm.nih.gov/pubmed/28818938)
  
  My main question is, **Which approaches should I use for filtering out bad cells in this case when we have multiple cell types in the dataset?**
  
  So far I tried to filter out genes that have too high mitochondrial genes content following the [Bioconductor “simpleSingleCell” workflow](https://www.bioconductor.org/help/workflows/simpleSingleCell/).
  
  However, the tutorial specifically says that the method of filtering out based on mitochondrial genes most probably will not work when the dataset has multiple cell types:
  
  > Analyzing all cell types together would unnecessarily inflate the MAD and
  > compromise the removal of low-quality cells, at best; or lead to the
  > entire loss of one cell type, at worst.
  
  Any suggestions would be greatly appreciated.
  
  **Tags:** rna-seq, filtering
  
  > **Comments:**
  > **username_1**: By filtering out what do you mean: removing the sample from the analysis when there are too many mithocondrial genes or removing the mitochondrial genes ? (This seems important in scRNAseq and I haven't worked with it, so excuse me if it is a naïve question)  
  > **username_0**: removing the bad quality samples  
  > **username_2**: Not a standard, but I found this course helpful http://hemberg-lab.github.io/scRNA.seq.course/ . I personally filter cells with too low or too high transcript counts, cells with low count of detected genes, and cells with high spike-in/endogenous RNA ratio. Prior to this pipeline I also filter out ribosomal RNA. Take it with a grain of salt because I'm still experimenting on it. Also, this answer may help https://bioinformatics.stackexchange.com/a/3171/1771  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2018-01-10. Score: 2
  
  From what I known, there is no clear consensus in the field and it depends on the type of cells you are interrogating.
  
  However, if mitoRNA/endogenousRNA ratio does not fit for your purposes, other option is to **check at the total number of genes/transcripts detected** in each cell. In this way, you can filter out cells that have considerable less genes/transcripts detected than the rest since this may be indicative of bad quality cells for any reason (apoptosis, RNA degradation, sequencing itself, etc). For instance, to **put a threshold** of >1000 genes/transcripts in a cell to be considered for further analysis.
  
  Consider also to take a look at the number of mapped reads for each cell, as cells with low mapped reads respect to the rest could be potentially problematic.
  
  > **Comments:**
  > **username_0**: What does it mean ‘mapped reads’? How is it different from the expression matrix itself?  
  > **username_3**: If you are using UMIs, usually I filter out those that are supported by less than 3 reads and some that do not fulfill QC requirements. In this case UMIs and mapped reads does not correspond (although should be very similar). At the end is another way of perform QC of the data but at an earlier stage of the analysis (before counting molecules and assign them to genes).  
  
  ---
  
  