.. Flair documentation master file, created by sphinx-quickstart on Fri Jul 8 08:42:03 2022. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Welcome to FLAIR's documentation! ================================= Staying in touch and getting help ================================= **Please subscribe to the FLAIR announce mailing list at:** FLAIR Announce Group https://groups.google.com/a/ucsc.edu/g/flair-announce-group This is a read-only, low volume list that will only have announcements of new FLAIR releases, publications, and other FLAIR-related user information. If you have questions, please ask in FLAIR GitHub Discussions: https://github.com/BrooksLabUCSC/flair/discussions Report bugs to FLAIR GitHub Issues: https://github.com/BrooksLabUCSC/flair/issues Installing FLAIR ================ FLAIR can be conda installed using .. code:: sh conda create -n flair -c conda-forge -c bioconda flair conda activate flair On Apple Silicon Mac systems (ARM64 CPUs: M1, M2, ...) you must use .. code:: sh CONDA_SUBDIR=osx-64 conda create -n flair conda activate flair conda config --env --set subdir osx-64 conda config --add channels bioconda conda config --add channels conda-forge conda install flair Note that mamba currently fails to install FLAIR on Mac ARM64. FLAIR can be run optionally with short-read data to help increase splice site accuracy of the long read splice junctions. FLAIR uses multiple alignment steps and splice site filters to increase confidence in the set of isoforms defined from noisy data. FLAIR was designed to be able to sense subtle splicing changes in nanopore data from `Tang et al. (2020) `__. Please read for more description of the methods. .. figure:: img/flair_workflow_compartmentalized.png If you have multiple samples and want to compare them on a single transcriptome, you have two options: Run flair correct and collapse individually on each sample, then combine your transcriptomes using ``collapse_bed_files`` (see Additional programs). This method will be faster and easier, but you may miss some low-expression transcripts. Your other option is to merge your samples before running FLAIR. If using PacBio reads, be careful doing this, as the reads may not have unique IDs. You may need to label each read with its sample ID to keep the read IDs unique. You can either merge the FASTA/FASTQ files before running FLAIR (simplest, recommended), or merge the bed files after running FLAIR correct, making sure to run FLAIR collapse with a list of all of your read files. It is recommended to combine all samples together prior to running ``flair-collapse`` for isoform assembly by concatenating corrected read ``bed`` files together. Following the creation of an isoform reference from ``flair-collapse``, consequent steps will assign reads from each sample individually to isoforms of the combined assembly for downstream analyses. .. toctree:: :maxdepth: 2 :caption: Contents: requirements.rst modules.rst scripts.rst flair2_functions.rst other_ways.rst other_environments.rst testrun.rst example_files.rst faqs.rst cite.rst Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`