Answers.Body: <p>I'll leave question 1 to someone else since I don't know. </p>
  
  <p>Regarding question 2, centromeric and telomeric regions are hard masked in hg19, so there's no sequence to repeat mask. </p>
  
  <p>For hg38, the centromeres are labeled <code>ALR/Alpha</code> with a class of <code>centr</code>. Telomeres are still hard-masked, but they tend to have simple repeats next to them (as annotated by repeatmasker, which makes sense).</p>
  
  <p>Apparently the <code>Other</code> class in hg19 is comprised of <a href="https://www.ncbi.nlm.nih.gov/pubmed/16288912" rel="nofollow noreferrer">SVA elements</a>. In hg38, these are reclassified as <code>Retrotransposon</code> class and <code>SVA</code> family, which didn't exist in hg19. </p>
  
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Answers.Text: > "Apparently the Other class in hg19 is comprised of SVA elements. In hg38, these are reclassified as Retrotransposon class and SVA family, which didn't exist in hg19."
  
  
  Interesting. Where did you find this information? Aren't SINE elements SVA elements?
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Answers.Text: Actually, do you have a citation for this? That's probably the most helpful addition to the answer above. "Apparently the Other class in hg19 is comprised of SVA elements. In hg38, these are reclassified as Retrotransposon class and SVA family, which didn't exist in hg19."
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Answers.Text: I don’t know that there’s anything to cite, this is an observation from looking at the annotations
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Answers.Text: Ah, you mean you're just looking at the `repName` for Other and extrapolating these must be SVA elements? You're right---these are SVA_A, SVA_B, SVA_C, SVA_D, SVA_E, SVA_F.
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Answers.Text: "Hard masked" means we know the sequences but mask them out for analysis purpose. We are unable to assemble most of hg19 centromeres, so we don't know these sequences. I wouldn't use "hard masked" here. We actually don't know hg38 centromeres, either. These are "manmade" sequences. See my answer below.
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Answers.Body: <p>On (2), centromeres and telomeres primarily consist of <a href="https://en.wikipedia.org/wiki/Satellite_DNA" rel="noreferrer">satellite</a> sequences. In human centromeres, the dominant type is alpha satellite (aka alphoid). GGAAT micro-satellite (aka SATIII centromeric micro-satellite) is also very common. There are less common types such as beta satellite. Because there are all kinds of centromeric/telomeric sequences of different lengths and properties, RepeatMasker doesn't put them into one class. Note that RepeatMasker has a "centr" class but it does not include all centromeric satellites (no SATIII, for example). In general, it is not advised to find centromeres with RepeatMasker output.</p>
  
  <p>GRCh38 is an unusual reference genome in that its centromeric sequences are computationally generated modeled after Venter as I remember. They are mostly alpha satellite, but are not real sequences (which has always bugged me). GRC know exactly where they put these sequences. GRCh37 is a more typical reference genome. It lacks probably majority of alpha satellites, but still has many. When you map reads to GRCh37, you occasionally see ~10,000-fold read depth even though the average depth is ~30X. These regions are mostly alpha satellites. Mappers just pile all different copies of satellites onto the ones remained in GRCh37.</p>
  
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Body: <p>I haven't been able to find the following in the documentation at <a href="http://www.repeatmasker.org/" rel="nofollow noreferrer">http://www.repeatmasker.org/</a> </p>
  
  <p>(1) Why are certain regions classified as "Other"? Are these regions impossible to concretely classify due to alignment issues?</p>
  
  <p>(2) I believe that centromeric and telomeric regions would be classified as tandem repeats. Are telomeric/centromeric regions classified as "DNA" within the hg19 version of RepeatMasker? </p>
  
  <p>Are these documented somewhere? </p>
  
Tags: <repeat><centromere><telomere>
Title: How are centromeric/telomeric regions categorized in RepeatMasker? "Other" category?
ThreadText: # How are centromeric/telomeric regions categorized in RepeatMasker? "Other" category?
  
  (Asked by: username_0 on 2017-09-28)
  
  I haven't been able to find the following in the documentation at <http://www.repeatmasker.org/>
  
  (1) Why are certain regions classified as "Other"? Are these regions impossible to concretely classify due to alignment issues?
  
  (2) I believe that centromeric and telomeric regions would be classified as tandem repeats. Are telomeric/centromeric regions classified as "DNA" within the hg19 version of RepeatMasker?
  
  Are these documented somewhere?
  
  **Tags:** repeat, centromere, telomere
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2017-09-28. Score: 3 | Accepted answer
  
  I'll leave question 1 to someone else since I don't know.
  
  Regarding question 2, centromeric and telomeric regions are hard masked in hg19, so there's no sequence to repeat mask.
  
  For hg38, the centromeres are labeled `ALR/Alpha` with a class of `centr`. Telomeres are still hard-masked, but they tend to have simple repeats next to them (as annotated by repeatmasker, which makes sense).
  
  Apparently the `Other` class in hg19 is comprised of [SVA elements](https://www.ncbi.nlm.nih.gov/pubmed/16288912). In hg38, these are reclassified as `Retrotransposon` class and `SVA` family, which didn't exist in hg19.
  
  > **Comments:**
  > **username_0**: > "Apparently the Other class in hg19 is comprised of SVA elements. In hg38, these are reclassified as Retrotransposon class and SVA family, which didn't exist in hg19."   Interesting. Where did you find this information? Aren't SINE elements SVA elements?  
  > **username_0**: Actually, do you have a citation for this? That's probably the most helpful addition to the answer above. "Apparently the Other class in hg19 is comprised of SVA elements. In hg38, these are reclassified as Retrotransposon class and SVA family, which didn't exist in hg19."  
  > **username_1**: I don’t know that there’s anything to cite, this is an observation from looking at the annotations  
  > **username_0**: Ah, you mean you're just looking at the `repName` for Other and extrapolating these must be SVA elements? You're right---these are SVA_A, SVA_B, SVA_C, SVA_D, SVA_E, SVA_F.  
  > **username_2**: "Hard masked" means we know the sequences but mask them out for analysis purpose. We are unable to assemble most of hg19 centromeres, so we don't know these sequences. I wouldn't use "hard masked" here. We actually don't know hg38 centromeres, either. These are "manmade" sequences. See my answer below.  
  
  ---
  
  ### Answer by username_2 on 2017-10-04. Score: 5
  
  On (2), centromeres and telomeres primarily consist of [satellite](https://en.wikipedia.org/wiki/Satellite_DNA) sequences. In human centromeres, the dominant type is alpha satellite (aka alphoid). GGAAT micro-satellite (aka SATIII centromeric micro-satellite) is also very common. There are less common types such as beta satellite. Because there are all kinds of centromeric/telomeric sequences of different lengths and properties, RepeatMasker doesn't put them into one class. Note that RepeatMasker has a "centr" class but it does not include all centromeric satellites (no SATIII, for example). In general, it is not advised to find centromeres with RepeatMasker output.
  
  GRCh38 is an unusual reference genome in that its centromeric sequences are computationally generated modeled after Venter as I remember. They are mostly alpha satellite, but are not real sequences (which has always bugged me). GRC know exactly where they put these sequences. GRCh37 is a more typical reference genome. It lacks probably majority of alpha satellites, but still has many. When you map reads to GRCh37, you occasionally see ~10,000-fold read depth even though the average depth is ~30X. These regions are mostly alpha satellites. Mappers just pile all different copies of satellites onto the ones remained in GRCh37.
  
  
  ---
  
  