From 99fd110c4b55fad3298d17f5ac5ecfc4f1b6f7e0 Mon Sep 17 00:00:00 2001 From: Matt Shirley Date: Tue, 28 May 2024 09:00:49 -0400 Subject: [PATCH 1/3] Update build_docs.yml --- .github/workflows/build_docs.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml index a9b0252..93f80c3 100644 --- a/.github/workflows/build_docs.yml +++ b/.github/workflows/build_docs.yml @@ -27,6 +27,9 @@ jobs: uses: r-lib/actions/setup-r@master with: r-version: '3.6.2' + + - name: Install renv + run: Rscript -e "install.packages(c('renv'), repos='https://cran.rstudio.com')" - name: Install python packages run: pip install tox From 8739201b818457ba7e2c9a08aa0f6f794b2778ee Mon Sep 17 00:00:00 2001 From: Matt Shirley Date: Tue, 28 May 2024 09:06:21 -0400 Subject: [PATCH 2/3] Update build_docs.yml --- .github/workflows/build_docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml index 93f80c3..ee2a79e 100644 --- a/.github/workflows/build_docs.yml +++ b/.github/workflows/build_docs.yml @@ -24,7 +24,7 @@ jobs: python-version: 3.9 - name: Setup R - uses: r-lib/actions/setup-r@master + uses: r-lib/actions/setup-r@v2 with: r-version: '3.6.2' From d6909a155d57679e8d81c9084e5f904fbdcd3ddb Mon Sep 17 00:00:00 2001 From: Matt Shirley Date: Tue, 28 May 2024 09:29:37 -0400 Subject: [PATCH 3/3] 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