Page 454genfusionen

This page is a collection of ideas concerning 454 RNA sequencing data analysis.

TODOs 25.3.:

General Questions

• which reference sequence (hg18/hg19)
• database for {mapped reads/ coverage, (predicted) transcripts/snps/indels, gene annotation}
• genome browser, visualization

Basic analysis

• number of mapped reads
• check coverage bzw depth for each mapping step (all steps combined)

Mapping steps

• spliced read mapping with gapped alignment
• local matches

Variant detection

• check if snpStore can handle 454 data (if not, adapt)
• fusion genes / alternative splicing

Plan 26.3.:

• normales mapping fuer 3 datensets laufen lassen (+ vorlaeufiges snp calling)
• split mapping mit edit distanz laufen lassen
• lokales mapping
• alle mappings kombinieren?
• snp calling

• splice varianten finden / genfusionen
• expression levels, coverage von genen
• insegt verstehen (sabrina krakau), evtl anpassen an gff format fuer mapped reads (→ wie sehen gesplicte reads aus (mehrere lokale hits)? verschiedene gene? verschiedene chromosomen? )
• gff-to-sam parser