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ProgressReportEmde-10-2010
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ProgressReportEmde
-10-2010
09 Aug 2023 - 17:03
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Progress Report
Accomplishments in the last six months:
Split read mapping:
Variant detection:
Ongoing data analysis projects:
SeqAn maintenance/ tutoring:
Other:
Goals for the next six months
Comments
Accomplishments in the last six months:
Split read mapping:
Finished implementation of splitRazers, poster at ISMB
Implemented sanity check perl script (using readsim to simulate split reads, split mapping, counting mapped reads)
Set up an evaluation pipeline:
simulate indels within given size ranges or from a gff file of known indels into a reference sequence (indelSimulator)
simulate reads from indeled reference (readsim)
map reads onto original reference (razers)
map leftover reads onto original reference (splitRazers)
do indel calling on split reads (snpStore)
check for TPs, FPs, FNs per size range (compareVariants)
Evaluated on simulated data:
simulated indels (size range -30 to 3000bp) --> almost everything can be recovered, and there are almost no FPs
simulate from dbSNP indels --> indels harder to
Comparison with GSNAP: work in progress (on 1. there were no big surprises)
Variant detection:
Added split-read indel calling in snpStore
Minor things like read clipping
Integrated realignment (finally!)
Ongoing data analysis projects:
Resequencing projects of Ropers department
Gene fusions in 454 RNA-Seq data (Lena Feldhahn, Tübingen)
SeqAn maintenance/ tutoring:
Seqan Retreat
Split-read mapping (hamming/edit) now in library/apps
SnpStore now in library/apps
Tutored Kerstin Neubert's Master thesis “Detection of copy number variations”
Other:
poster at ISMB 2010, Illumina meeting,
SeqAn
retreat
Reviewed 2 papers
Incorporated self-matches in refinement and corresponding self-edges in alignment graph
Goals for the next six months
Finish paper on splitRazers, submit before Christmas
With Birte: Split mapping with local swift (multiply split reads)
Start writing up thesis after Christmas break
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