From ae35f146c1fc0c2359b87c309d2a5ac2a756b4ac Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Thu, 3 Aug 2023 17:53:07 +0200 Subject: [PATCH] Add information about missing files for elution-only runs. --- docs/pvacbind/output_files.rst | 5 ++++- docs/pvacfuse/output_files.rst | 5 ++++- docs/pvacseq/output_files.rst | 13 +++++++++---- 3 files changed, 17 insertions(+), 6 deletions(-) diff --git a/docs/pvacbind/output_files.rst b/docs/pvacbind/output_files.rst index 5af11239..b132d5ec 100644 --- a/docs/pvacbind/output_files.rst +++ b/docs/pvacbind/output_files.rst @@ -28,7 +28,7 @@ created): predictions added. * - ``.all_epitopes.aggregated.tsv`` - An aggregated version of the ``all_epitopes.tsv`` file that gives information about - the best epitope for each mutation in an easy-to-read format. + the best epitope for each mutation in an easy-to-read format. Not generated when running with elution algorithms only. * - ``.all_epitopes.aggregated.tsv.reference_matches`` (optional) - A file outlining details of reference proteome matches @@ -75,6 +75,9 @@ _______________________________________________ - NetMHCpanEL - NetMHCIIpanEL +Please note that when running pVACfuse with only elution algorithms, no +aggregate report is created. + .. _pvacbind_all_ep_and_filtered: all_epitopes.tsv and filtered.tsv Report Columns diff --git a/docs/pvacfuse/output_files.rst b/docs/pvacfuse/output_files.rst index ffb93d07..aebcc449 100644 --- a/docs/pvacfuse/output_files.rst +++ b/docs/pvacfuse/output_files.rst @@ -39,7 +39,7 @@ created): predictions added. * - ``.all_epitopes.aggregated.tsv`` - An aggregated version of the ``all_epitopes.tsv`` file that gives information about - the best epitope for each mutation in an easy-to-read format. + the best epitope for each mutation in an easy-to-read format. Not generated when running with elution algorithms only. * - ``.all_epitopes.aggregated.tsv.reference_matches`` (optional) - A file outlining details of reference proteome matches @@ -89,6 +89,9 @@ _______________________________________________ - NetMHCpanEL - NetMHCIIpanEL +Please note that when running pVACfuse with only elution algorithms, no +aggregate report is created. + all_epitopes.tsv and filtered.tsv Report Columns ------------------------------------------------ diff --git a/docs/pvacseq/output_files.rst b/docs/pvacseq/output_files.rst index b94321cb..baf12a61 100644 --- a/docs/pvacseq/output_files.rst +++ b/docs/pvacseq/output_files.rst @@ -43,18 +43,20 @@ created): predictions, and reference proteome similarity metrics added. * - ``.all_epitopes.aggregated.tsv`` - An aggregated version of the ``all_epitopes.tsv`` file that gives information about - the best epitope for each mutation in an easy-to-read format. + the best epitope for each mutation in an easy-to-read format. Not + generated when running with elution algorithms only. * - ``.all_epitopes.aggregated.tsv.reference_matches`` (optional) - A file outlining details of reference proteome matches * - ``.all_epitopes.aggregated.metrics.json`` - A JSON file with detailed information about the predicted epitopes, formatted for pVACview. This file, in combination with the aggregated.tsv file, is required to visualize your results - in pVACview. + in pVACview. Not generated when running with elution algorithms only. * - ``ui.R``, ``app.R``, ``server.R``, ``styling.R``, ``anchor_and_helper_functions.R`` - - pVACview R Shiny application files + - pVACview R Shiny application files. Not generated when running with elution algorithms only. * - ``www`` (directory) - - Directory containing image files for pVACview + - Directory containing image files for pVACview. Not generated when running with elution algorithms only. + Filters applied to the filtered.tsv file ---------------------------------------- @@ -101,6 +103,9 @@ _______________________________________________ - NetMHCpanEL - NetMHCIIpanEL +Please note that when running pVACseq with only elution algorithms, no +aggregate report and pVACview files are created. + .. _all_ep_and_filtered: all_epitopes.tsv and filtered.tsv Report Columns