Brendel Group Presentation: 6 Mar 2013

216 views

Published on

Results from applying Trinity's 3 transcript construction algorithms on an RNA-Seq data set.

Published in: Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
216
On SlideShare
0
From Embeds
0
Number of Embeds
2
Actions
Shares
0
Downloads
5
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Brendel Group Presentation: 6 Mar 2013

  1. 1. Comparison of transcriptome assemblies produced by different Trinity transcript construction algorithms Daniel Standage Brendel Group, Indiana University 6 Mar 2014 Daniel Standage (Brendel Group @ IU) Trinity Assembly 6 Mar 2014 1 / 16
  2. 2. Summary Three different construction approaches Butterfly: enumerate all plausible transcripts with minimal read support PASA: for each alignment, find largest assembly (transcript) containing the alignment CuffLinks: find minimal assembl(y|ies) that explain the data, using read coverage to “phase” distant exons Daniel Standage (Brendel Group @ IU) Trinity Assembly 6 Mar 2014 2 / 16
  3. 3. Summary Comparison of 8 Trinity assemblies Hypotheses (transcripts per assembly) Butterfly > PasaFly > CuffFly Diginorm > No diginorm Daniel Standage (Brendel Group @ IU) Trinity Assembly 6 Mar 2014 3 / 16
  4. 4. Summary Comparison of 8 Trinity assemblies Comparison matrix Diginorm Butterfly --PasaFly --CuffFly Butterfly --min kmer cov 2 Daniel Standage (Brendel Group @ IU) version version version version Trinity Assembly 0.1.1 0.1.2 0.1.3 0.1.4 + version 0.2.1 version 0.2.2 version 0.2.3 version 0.2.4 6 Mar 2014 4 / 16
  5. 5. Summary Transcript sequences per assembly Diginorm Butterfly --PasaFly --CuffFly Butterfly --min kmer cov 2 Daniel Standage (Brendel Group @ IU) Trinity Assembly 241,851 169,754 161,921 209,355 + 476,234 191,468 173,407 433,399 6 Mar 2014 5 / 16
  6. 6. Summary Assembly size Diginorm Butterfly --PasaFly --CuffFly Butterfly --min kmer cov 2 Daniel Standage (Brendel Group @ IU) Trinity Assembly 458M 169M 137M 445M + 1.5G 269M 176M 1.4G 6 Mar 2014 6 / 16
  7. 7. Summary Transcripts aligned to PdomSCFr1.1-0002 Diginorm Butterfly --PasaFly --CuffFly Butterfly --min kmer cov 2 Daniel Standage (Brendel Group @ IU) 5,197 3,752 3,612 5,102 Trinity Assembly (2.1%) (2.2%) (2.2%) (2.4%) + 12,160 (2.6%) 4,030 (2.1%) 3,620 (2.1%) 11,727 (2.7%) 6 Mar 2014 7 / 16
  8. 8. Summary Visual inspection http://goblinx3.soic.indiana.edu/GDB001/ Daniel Standage (Brendel Group @ IU) Trinity Assembly 6 Mar 2014 8 / 16
  9. 9. Beyond visual inspection Beyond visual inspection More scalable assessment needed Can I compute statistics to summarize (visually) observed patterns? How can I leverage additional information (such as alignment quality)? Daniel Standage (Brendel Group @ IU) Trinity Assembly 6 Mar 2014 9 / 16
  10. 10. Beyond visual inspection Initial ideas Distribution Distribution Distribution Distribution Distribution Daniel Standage (Brendel Group @ IU) of of of of of exon quality intron quality exons per transcript transcripts per locus transcript similarity Trinity Assembly 6 Mar 2014 10 / 16
  11. 11. Beyond visual inspection Intron quality: donor site P-values Daniel Standage (Brendel Group @ IU) Trinity Assembly 6 Mar 2014 11 / 16
  12. 12. Beyond visual inspection Intron quality: acceptor site P-values Daniel Standage (Brendel Group @ IU) Trinity Assembly 6 Mar 2014 12 / 16
  13. 13. Beyond visual inspection Exons per alignment Daniel Standage (Brendel Group @ IU) Trinity Assembly 6 Mar 2014 13 / 16
  14. 14. Observations Observations --PasaFly and --CuffFly are more conservative --PasaFly and --CuffFly appear robust to diginorm Daniel Standage (Brendel Group @ IU) Trinity Assembly 6 Mar 2014 14 / 16
  15. 15. Observations Discussion Why not implement an EM algorithm to discern differential isoforms and identify primary isoform? Daniel Standage (Brendel Group @ IU) Trinity Assembly 6 Mar 2014 15 / 16
  16. 16. Observations Thank you! Daniel Standage (Brendel Group @ IU) Trinity Assembly 6 Mar 2014 16 / 16

×