From 3a34b5c65c87325f6108a98ed9e5923c8719cde2 Mon Sep 17 00:00:00 2001 From: Aris Paschalidis Date: Mon, 15 Nov 2021 11:55:19 -0500 Subject: [PATCH] Add a files generated section --- docs/files-generated.rst | 96 ++++++++++++++++++++++++++++++++++++++++ docs/index.rst | 6 +++ 2 files changed, 102 insertions(+) create mode 100644 docs/files-generated.rst diff --git a/docs/files-generated.rst b/docs/files-generated.rst new file mode 100644 index 0000000..085db7e --- /dev/null +++ b/docs/files-generated.rst @@ -0,0 +1,96 @@ +.. _files_generated: + +=============== +Files Generated +=============== + +Here, we provide a list of all files generated by MIPTools and a brief +description of each file. This list aims to assist users in determining the +most useful output for downstream analysis. + +Non-aggregate Tables +==================== + +alternate_table + insert description + +coverage_table + insert description + +genotypes_table + insert description + +reference_table + insert description + +Aggregate Amino Acid Changes +============================ + +alternate_AA_table + insert description + +coverage_AA_table + insert description + +genotypes_AA_table + insert description + +reference_AA_table + insert description + +Aggregate Nucleotide Changes +============================ + +alternate_AN_table + insert description + +coverage_AN_table + insert description + +genotypes_AN_table + insert description + +reference_AN_table + insert description + +Haplotype Files +=============== + +aligned_haplotypes + insert description + +all_haplotypes + insert description + +haplotype_counts + insert description + +mapped_haplotypes + insert description + +offtarget_haplotypes + insert description + +unique_haplotypes + insert description + +Barcode Files +============= + +all_barcode_counts + insert description + +barcode_counts + insert description + +Sequence Run Files +================== + +repool + insert description + +run_meta + insert description + +sample_summary + insert description diff --git a/docs/index.rst b/docs/index.rst index 3905f56..7537fd3 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -13,6 +13,12 @@ inversion probe design, data processing, and analysis. installation quick_start +.. toctree:: + :caption: Glossary + :maxdepth: 1 + + files-generated + Need Help? ----------