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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0
author iuc
date Fri, 04 Apr 2025 10:37:49 +0000
parents 98163e8ed458
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4:98163e8ed458 5:5e03d09d5fdc
505 It is based on chimeric alignments found by the STAR RNA-Seq aligner. 505 It is based on chimeric alignments found by the STAR RNA-Seq aligner.
506 506
507 507
508 **INPUTS** 508 **INPUTS**
509 509
510 See: https://arriba.readthedocs.io/en/latest/input-files/ 510 See: https://github.com/suhrig/arriba/wiki/04-Input-files
511 511
512 - Alignments 512 - Alignments
513 513
514 Arriba takes the main output file of STAR (Aligned.out.bam) as input (parameter -x). If STAR was run with the parameter --chimOutType WithinBAM, then this file contains all the information needed by Arriba to find fusions. When STAR was run with the parameter --chimOutType SeparateSAMold, the main output file lacks chimeric alignments. Instead, STAR writes them to a separate output file named Chimeric.out.sam. In this case, the file needs to be passed to Arriba via the parameter -c in addition to the main output file Aligned.out.bam. 514 Arriba takes the main output file of STAR (Aligned.out.bam) as input (parameter -x). If STAR was run with the parameter --chimOutType WithinBAM, then this file contains all the information needed by Arriba to find fusions. When STAR was run with the parameter --chimOutType SeparateSAMold, the main output file lacks chimeric alignments. Instead, STAR writes them to a separate output file named Chimeric.out.sam. In this case, the file needs to be passed to Arriba via the parameter -c in addition to the main output file Aligned.out.bam.
515 515
670 NOTE: Arriba was designed for alignments from RNA-Seq data. It should not be run on WGS data directly. Many assumptions made by Arriba about the data (statistical models, blacklist, etc.) only apply to RNA-Seq data and are not valid for DNA-Seq data. For such data, a structural variant calling algorithm should be used and the results should be passed to Arriba. 670 NOTE: Arriba was designed for alignments from RNA-Seq data. It should not be run on WGS data directly. Many assumptions made by Arriba about the data (statistical models, blacklist, etc.) only apply to RNA-Seq data and are not valid for DNA-Seq data. For such data, a structural variant calling algorithm should be used and the results should be passed to Arriba.
671 671
672 672
673 **OPTIONS** 673 **OPTIONS**
674 674
675 - Arriba: https://arriba.readthedocs.io/en/latest/command-line-options/#arriba 675 - Arriba: https://github.com/suhrig/arriba/wiki/07-Command-line-options#arriba
676 - Visualization: https://arriba.readthedocs.io/en/latest/command-line-options/#draw_fusionsr 676 - Visualization: https://github.com/suhrig/arriba/wiki/07-Command-line-options#draw_fusionsr
677 - RNA STAR: https://arriba.readthedocs.io/en/latest/workflow/ 677 - RNA STAR: https://github.com/suhrig/arriba/wiki/03-Workflow
678 678
679 679
680 **OUTPUTS** 680 **OUTPUTS**
681 681
682 See: https://arriba.readthedocs.io/en/latest/output-files/ 682 See: https://github.com/suhrig/arriba/wiki/05-Output-files
683 683
684 - fusions.tsv 684 - fusions.tsv
685 685
686 The file fusions.tsv (as specified by the parameter -o) contains fusions which pass all of Arriba's filters. It should be highly enriched for true predictions. The predictions are listed from highest to lowest confidence. The following paragraphs describe the columns in detail: 686 The file fusions.tsv (as specified by the parameter -o) contains fusions which pass all of Arriba's filters. It should be highly enriched for true predictions. The predictions are listed from highest to lowest confidence. The following paragraphs describe the columns in detail:
687 687
730 The file fusions.discarded.tsv (as specified by the parameter -O) contains all events that Arriba classified as an artifact or that are also observed in healthy tissue. It has the same format as the file fusions.tsv. 730 The file fusions.discarded.tsv (as specified by the parameter -O) contains all events that Arriba classified as an artifact or that are also observed in healthy tissue. It has the same format as the file fusions.tsv.
731 731
732 732
733 **VISUALIZATION** 733 **VISUALIZATION**
734 734
735 See: https://arriba.readthedocs.io/en/latest/visualization/ 735 See: https://github.com/suhrig/arriba/wiki/06-Visualization
736 736
737 - fusions.pdf 737 - fusions.pdf
738 738
739 A PDF file with one page for each predicted fusion. Each page depicts the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and if the column fusion_transcript has a value an excerpt of the sequence around the breakpoint. 739 A PDF file with one page for each predicted fusion. Each page depicts the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and if the column fusion_transcript has a value an excerpt of the sequence around the breakpoint.
740 740
741 .. image:: draw-fusions-example.png 741 .. image:: draw-fusions-example.png
742 :width: 800 742 :width: 800
743 :height: 467 743 :height: 467
744 744
745 745
746 .. _Arriba: https://arriba.readthedocs.io/en/latest/ 746 .. _Arriba: https://github.com/suhrig/arriba/wiki/01-Home
747 .. _INPUTS: https://arriba.readthedocs.io/en/latest/input-files/ 747 .. _INPUTS: https://github.com/suhrig/arriba/wiki/04-Input-files
748 .. _OUTPUTS: https://arriba.readthedocs.io/en/latest/output-files/ 748 .. _OUTPUTS: https://github.com/suhrig/arriba/wiki/05-Output-files
749 .. _VISUALIZATION: https://arriba.readthedocs.io/en/latest/visualization/ 749 .. _VISUALIZATION: https://github.com/suhrig/arriba/wiki/06-Visualization
750 .. _OPTIONS: https://arriba.readthedocs.io/en/latest/command-line-options/ 750 .. _OPTIONS: https://github.com/suhrig/arriba/wiki/07-Command-line-options
751 751
752 ]]></help> 752 ]]></help>
753 <expand macro="citations" /> 753 <expand macro="citations" />
754 </tool> 754 </tool>