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docs/content/Bioinformatics_tools/isoquant.rst

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+long-read RNA-seq quantification
+===============================
+
+
+Summary
+^^^^^^^
+
+long-read RNA-seq quantification using isoQuant
+
+
+Input
+^^^^^
+
+
+Fastq files. Need to have ``fastq`` in the filename. e.g., .fastq or .fastq.gz
+
+
+Usage
+^^^^^
+
+Copy the ``*fastq*`` files into the working dir.
+
+.. code:: bash
+
+	hpcf_interactive.sh
+
+	module load python/2.7.13
+
+	# cd to your working dir
+
+	run_lsf.py -p isoQuant
+
+Output
+^^^^^
+
+In the jobID folder, see ``OUT.transcript_grouped_tpm.tsv`` or ``OUT.gene_grouped_tpm.tsv``
+
+Comments
+^^^^^^^^
+
+.. disqus::
+    :disqus_identifier: NGS_pipelines
+
+
+
+
+
+
+
+
+
+
+
+