Appendix
=====================

.. contents:: 
   :depth: 2

Correspondence table for the genome build
---------------------------------------------------

While ``download_genomedata.sh`` uses the `Ensembl <https://asia.ensembl.org/index.html>`_ genome build, **Churros** uses `UCSC <https://genome.ucsc.edu/>`_ genome build in the command. Here we summarize the correspondence.

.. csv-table::
   :class: align-center

   "**Species**", "**Ensembl**", "**UCSC**"
   "human", "GRCh38", "hg38"
   "human", "GRCh37", "hg19"
   "mouse", "GRCm39", "mm39"
   "mouse", "GRCm38", "mm10"
   "rat",   "mRatBN7.2", "rn7"
   "fly",   "BDGP6",  "dm6"
   "zebrafish", "GRCz11", "danRer11"
   "chicken", "GRCg6a", "galGal6"
   "C.elegans", "WBcel235", "ce11"
   "S.serevisiae", "R64-1-1", "sacCer3"
   "African clawed frog", "Xenopus_tropicalis", "xenLae2"

For example, to use human genome build GRCh38/hg38, specify GRCh38 or hg38 for ``download_genomedata.sh`` and hg38 for ``churros``.

.. code-block:: bash

   download_genomedata.sh hg38 UCSC-hg38/ 2>&1 | tee log/UCSC-hg38
   churros -p 24 --mpbl samplelist.txt samplepairlist.txt hg38 UCSC-hg38
   # or
   download_genomedata.sh GRCh38 Ensembl-GRCh38/ 2>&1 | tee log/Ensembl-GRCh38
   churros -p 24 --mpbl samplelist.txt samplepairlist.txt hg38 Ensembl-GRCh38/

Other species: 

.. csv-table::
   :class: align-center
   
   "**Species**", "**ID**"
   "human", "T2T"
   "S.pombe", "SPombe"
   "A.thaliana", "TAIR10"
   "Oryzias latipes", "Medaka"
   "Hydra vulgaris AEP", "HVAEP"