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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 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?

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    $\begingroup$ Have you considered emailing 10xGenomics and asking? You're already paying them money for their products, so they'll reply. $\endgroup$
    – Devon Ryan
    Jun 9, 2017 at 9:19
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    $\begingroup$ 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. $\endgroup$
    – Glrs
    Jun 9, 2017 at 9:27
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    $\begingroup$ 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. $\endgroup$
    – Devon Ryan
    Jun 9, 2017 at 9:30
  • $\begingroup$ 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? $\endgroup$
    – Glrs
    Jun 9, 2017 at 9:39
  • $\begingroup$ 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. $\endgroup$
    – Devon Ryan
    Jun 9, 2017 at 9:41

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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).

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