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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit d2317dff5a89016f18038b97d057f47d949e7808-dirty
author jjohnson
date Sat, 26 Jan 2019 12:53:08 -0500
parents b22f8634ff84
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16:bdd93719cede 17:c3167ccca38c
59 Reference Dataset 59 Reference Dataset
60 The reference dataset setup process has been simplified as of deFuse 0.6.0, and deFuse now automatically downloads all required files. 60 The reference dataset setup process has been simplified as of deFuse 0.6.0, and deFuse now automatically downloads all required files.
61 The create_reference_dataset.pl script will download the genome and other source files, and build any derivative files including bowtie indices, gmap indices, and 2bit files. Run the following command. Expect this step to take at least 12 hours. 61 The create_reference_dataset.pl script will download the genome and other source files, and build any derivative files including bowtie indices, gmap indices, and 2bit files. Run the following command. Expect this step to take at least 12 hours.
62 create_reference_dataset.pl -c config.txt 62 create_reference_dataset.pl -c config.txt
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65 defuse_trinity_analysis.py - Validating deFuse predictions using Trinity de novo assembled transcripts
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67 DeFuse provides a total fusion sequence of 200-500 nucleotides (nts) around the fusion breakpoint. This may be insufficient to predict the effect of the fusion on protein production. To get a view of the full transcript containing the fusion, Trinity de novo transcripts from the RNA-seq data are compared with the deFuse fusion sequences using a subsequence around the deFuse indetified fusion breakpoint. The Trinity transcriptToOrfs output provides potential proteins from the projected fusion transcript.
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