Domanda:
Quali strumenti possono rilevare l'RNA chimerico (geni di fusione) dai dati WGS o RNA-Seq?
L42
2017-05-31 15:05:01 UTC
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Dati i dati WGS o i dati RNA-seq, quali strumenti posso utilizzare per rilevare le fusioni geniche?

Due risposte:
#1
+9
L42
2017-05-31 15:05:01 UTC
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La maggior parte di questi utilizza dati RNA-seq, alcuni utilizzano dati WGS e altri entrambi. Sono elencati in ordine alfabetico. Aggiungerò alla lista quando scoprirò di più.

  1. Barnacle: http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-550
  2. Bellerophontes: http://bioinformatics.oxfordjournals.org/content/28/16/2114.long
  3. BreakDancer: http: //www.nature.com/nmeth/journal/v6/n9/abs/nmeth.1363.html
  4. BreakFusion: http: //www.ncbi.nlm.nih .gov / pmc / articles / PMC3389765 /
  5. BreakPointer: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561864/
  6. ChimeraScan: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187648/
  7. Compagno: http: / /bioinformatics.oxfordjournals.org/content/27/11/1481.long
  8. CRAC: http://www.ncbi.nlm.nih.gov/pmc/articles/ PMC4053775 /
  9. deFuse: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001138
  10. Dissect: http://bioinformatics.oxfordjournals.org/content/28/12/i179.abstract
  11. EBARDenovo: http: //bioinformatics.oxfordjournals. org / conten t / early / 2013/03/01 / bioinformatics.btt092
  12. EricScript: http://bioinformatics.oxfordjournals.org/content/28/24/3232
  13. FusionAnalyser: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439881/
  14. FusionCatcher: http: //biorxiv.org/content/early/2014/11/19/011650.full-text.pdf+html
  15. FusionFinder: http: //www.ncbi.nlm .nih.gov / pmc / articoli / PMC3384600 /
  16. FusionHunter: http://bioinformatics.oxfordjournals.org/content/27/12/1708.long
  17. FusionMap: http://bioinformatics.oxfordjournals.org/content/27/14/1922
  18. FusionQ: http: // www .biomedcentral.com / 1471-2105 / 14/193
  19. FusionSeq: http://www.genomebiology.com/2010/11/10/R104
  20. IDP-fusion: http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv562.full
  21. iFUSE: http://bioinformatics.oxfordjournals.org/content/29/13/1700.long
  22. InFusion: https://bitbucket.org / kokonech / infusion / wiki / Home
  23. INTEGRARE: http://www.ncbi.nlm.nih.gov/pubmed/26556708
  24. JAFFA: http://www.genomemedicine.com/content/7/1/43
  25. LifeScope: http://www.thermofisher.com/ no / it / home / scienze della vita / sequencing / next-generation-sequencing / solid-next-generation-sequencing / solid-next-generation-sequencing-data-analysis-solutions / lifescope-data-analysis-solid-next- generation-sequencing / lifescope-genomic-analysis-software-solid-next-generation-sequencing.html
  26. MapSplice: http://www.ncbi.nlm.nih.gov / pubmed / 20802226
  27. MOJO https://github.com/cband/MOJO
  28. nFuse: http: // www.ncbi.nlm.nih.gov/pmc/articles/PMC3483554/
  29. Pegasus: http://www.biomedcentral.com/1752-0509/8/97
  30. PRADA: http://www.ncbi.nlm.nih.gov/pubmed/24695405
  31. ShortFuse: http: //www.ncbi.n lm.nih.gov/pmc/articles/PMC3072550/
  32. SnowShoes-FTD: http://nar.oxfordjournals.org/content/39/15/e100
  33. SOAPFuse: http://www.genomebiology.com/2013/14/2/R12
  34. SOAPFusion: http: // www.ncbi.nlm.nih.gov/pubmed/24123671
  35. STAR: http://bioinformatics.oxfordjournals.org/content/29/1/15
  36. STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion/wiki
  37. TopHat-Fusion: http : //www.ncbi.nlm.nih.gov/pmc/articles/PMC3245612/
  38. TRUP: http://www.genomebiology.com/2015/16/1 / 7
  39. ViralFusionSeq: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582262/

Altri programmi utili:

Chimeraviz (strumenti di visualizzazione per fusioni geniche): https://www.ncbi.nlm.nih.gov/pubmed/28525538 (disclaimer: ho creato questo)

Chimera: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253834/
OncoFuse: http://bioinformatics.oxfordjournals.org/content/29/20/2539.long
FuMa: http://bioinformatics.oxfordjournals.org/content/early/2015/12/09/bioinformatics.btv721.abstract

#2
  0
glyph
2017-05-31 21:58:31 UTC
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1- Chimerascan + Star

2- Tophat Fusion

Due pipeline che ho usato ampiamente e che consiglio. Con gli altri elencati da @ L42 non posso parlare ma Star Fusion sembra promettente. Star è veloce.



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