Answers.Body: <p>You can see the exact assembly by looking in the README file in Ensembl's genome download page. <a href="ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/README" rel="nofollow noreferrer">ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/README</a></p>
  
  <p>As you can see the current assembly is GCA_000001405.25. Ensembl 79 uses version GCA_000001405.17. You can expect some differences between assembly versions. </p>
  
  <p>If you take a look at <a href="https://www.ncbi.nlm.nih.gov/assembly?term=GRCh38&amp;cmd=DetailsSearch" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/assembly?term=GRCh38&amp;cmd=DetailsSearch</a> </p>
  
  <p>You can see that 20,466,394 bp have been added since 17 -> 25. This is only about 0.6% change so I would guess there is not that much difference between these versions. However, if I were you I would use the corresponding version of Ensembl. Even better would be using the latest version of Ensembl, as not only the genomes primary sequence but also the positions of genes can change between versions (<a href="https://doi.org/10.1093/bib/bbw017" rel="nofollow noreferrer">https://doi.org/10.1093/bib/bbw017</a>). </p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-10T23:09:04.270Z
Answers.LastActivityDate: 2017-06-10T23:09:04.270Z
Answers.UserDisplayName: tweirick
Body: <p>I got a customized GRCh38.79 .gtf file (modified to have no MT genes) and I need to create a reference genome out of it (for 10xGenomics CellRanger pipeline). I suspect that the .79 part is the Ensembl number, which according this <a href="http://www.ensembl.org/Help/ArchiveList" rel="nofollow noreferrer">ensembl archive list</a> is paired with the GRCh38.p2 patch.</p>
  
  <p>Should I use this patch's fasta file, or it would be fine to use any of the GRCh38 patches?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-09T09:19:21.840Z
Comments.Text: Have you considered emailing 10xGenomics and asking? You're already paying them money for their products, so they'll reply.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-09T09:27:52.950Z
Comments.Text: I know how to make the reference genome using cellranger, in which case they could help. My question is more on how the GRCh## versioning works, for which I think here is a better and definitely faster place to ask rather than 10xGenomics.
Comments.UserDisplayName: Glrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-09T09:30:01.310Z
Comments.Text: The different Ensembl releases are associated to genome patches with different patch contigs, so it becomes a question whether their software can handle missing contigs.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-09T09:39:12.413Z
Comments.Text: Okay, right! This is a question I should ask them. Thanks @DevonRyan . However, if their answer is positive, would it still be significantly better to use both parts of the same release, or it doesn't make that much of a difference?
Comments.UserDisplayName: Glrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-09T09:41:38.860Z
Comments.Text: If it doesn't break their software then it shouldn't matter either way :) In reality, it's trivial to strip a whole chromosome out of a GTF, so just use GTF/fasta from the most recent Ensembl release and you'll get slightly more reliable results.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-09T09:42:03.063Z
Comments.Text: BTW, feel encouraged to post their reply, since then it'll be indexed on google.
Comments.UserDisplayName: Devon Ryan
Tags: <human-genome><reference-genome><gtf><10x-genomics>
Title: Can a customized GRCh38 .gtf file be used with any of the GRCh38 released patches?
ThreadText: # Can a customized GRCh38 .gtf file be used with any of the GRCh38 released patches?
  
  (Asked by: username_0 on 2017-06-09)
  
  I got a customized GRCh38.79 .gtf file (modified to have no MT genes) and I need to create a reference genome out of it (for 10xGenomics CellRanger pipeline). I suspect that the .79 part is the Ensembl number, which according this [ensembl archive list](http://www.ensembl.org/Help/ArchiveList) is paired with the GRCh38.p2 patch.
  
  Should I use this patch's fasta file, or it would be fine to use any of the GRCh38 patches?
  
  **Tags:** human-genome, reference-genome, gtf, 10x-genomics
  
  > **Comments:**
  > **username_1**: Have you considered emailing 10xGenomics and asking? You're already paying them money for their products, so they'll reply.  
  > **username_0**: I know how to make the reference genome using cellranger, in which case they could help. My question is more on how the GRCh## versioning works, for which I think here is a better and definitely faster place to ask rather than 10xGenomics.  
  > **username_1**: The different Ensembl releases are associated to genome patches with different patch contigs, so it becomes a question whether their software can handle missing contigs.  
  > **username_0**: Okay, right! This is a question I should ask them. Thanks @username_1 . However, if their answer is positive, would it still be significantly better to use both parts of the same release, or it doesn't make that much of a difference?  
  > **username_1**: If it doesn't break their software then it shouldn't matter either way :) In reality, it's trivial to strip a whole chromosome out of a GTF, so just use GTF/fasta from the most recent Ensembl release and you'll get slightly more reliable results.  
  > **username_1**: BTW, feel encouraged to post their reply, since then it'll be indexed on google.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2017-06-10. Score: 2
  
  You can see the exact assembly by looking in the README file in Ensembl's genome download page. <ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/README>
  
  As you can see the current assembly is GCA\_000001405.25. Ensembl 79 uses version GCA\_000001405.17. You can expect some differences between assembly versions.
  
  If you take a look at <https://www.ncbi.nlm.nih.gov/assembly?term=GRCh38&cmd=DetailsSearch>
  
  You can see that 20,466,394 bp have been added since 17 -> 25. This is only about 0.6% change so I would guess there is not that much difference between these versions. However, if I were you I would use the corresponding version of Ensembl. Even better would be using the latest version of Ensembl, as not only the genomes primary sequence but also the positions of genes can change between versions (<https://doi.org/10.1093/bib/bbw017>).
  
  
  ---
  
  