Page ProgressReportEmde-04-2010

Progress report

Accomplishments in the last six months:

General:

• Read many papers on variant detection, notes taken here.
• Implemented (and bug-fixed various times) split-read mapping (hamming/edit), integrated into MPI-variant-detection-pipeline
• Integrated realignment into snp calling (but still not really giving the expected results... TODO!)

Ongoing data analysis projects:

• Resequencing projects of Ropers department
• Mutation detection in miRNA (Marcel Grunert)
• Gene fusions in 454 RNA-Seq data (Lena Feldhahn, Tübingen)

SeqAn maintenance/ tutoring:

• Tutorial + some code documenting/cleaning
• Tutored Master thesis “Methods for multi-read assignment”
• Tutoring Master thesis “Detection of copy number variations”

Goals for the next six months

• Evaluation of variation detection methods (especially indel detection with split reads)
• Make poster (ISMB)
• With Birte: Spliced mapping with local swift (multiply spliced reads)
• Paper about split mapping (or two papers?)

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