From d6909a155d57679e8d81c9084e5f904fbdcd3ddb Mon Sep 17 00:00:00 2001 From: Matt Shirley Date: Tue, 28 May 2024 09:29:37 -0400 Subject: [PATCH] Add section describing composite transcriptomes --- .gitignore | 3 ++- docsource/running.rst | 10 ++++++++++ 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 436ac46..e1d07cb 100644 --- a/.gitignore +++ b/.gitignore @@ -5,4 +5,5 @@ build dist docs -*.egg-info \ No newline at end of file +*.egg-info +.vscode/settings.json diff --git a/docsource/running.rst b/docsource/running.rst index 59649fe..68fcc09 100644 --- a/docsource/running.rst +++ b/docsource/running.rst @@ -65,6 +65,16 @@ explicitly, or default to automatic values. .. command-output:: pisces run --help +The (``-t, --sample-type``) flag is used to specify the species name, +which will select the index files ``salmon quant`` uses to quantify transcript expression from the selected +set of fastq files. The species name is the top level key in the :doc:`config` file. If the ``--sample-type`` +defines a transcriptome composed of transcripts from multiple species/assemblies (GTF/FASTA pairs), the +transcript expression will be quantified using a single combined index with transcript abundance jointly +calculated on all transcripts from the composite transcriptome. The ``pisces summarize-expression`` command will separate transcript and gene +expression estimantes (counts and TPM) into separate output tables for each species/assembly and re-scale TPM values as if the +transcript and gene expression were estimated independently. This method ensures that sequence reads which map ambiguously +between similar transcripts will be assigned to the most likely transcript during quantification. + .. _submit_example: pisces submit