Benchmarking of read mapping bias in allele specific expression analysis

Visa enkel post
dc.contributor.authorJames, Alva Rani
dc.contributor.departmentChalmers tekniska högskola / Institutionen för matematiska vetenskapersv
dc.contributor.departmentChalmers University of Technology / Department of Mathematical Sciencesen
dc.date.accessioned2019-07-03T13:11:06Z
dc.date.available2019-07-03T13:11:06Z
dc.date.issued2013
dc.description.abstractMost genes in diploid organisms have two “copies”; one copy inherited from each parent. If an individual has two different alleles (code variants) at a specific gene locus, then the individual is heterozygous at that locus. Allele specific expression (ASE) can be explained as the differential expression between the two different alleles of a gene in a single individual. There are several mechanisms that can cause ASE, e. g, it can be caused by a heterozygous variant in the promoter region, causing a difference in transcription factor binding affinity between the maternal and paternal allele. Accurate measurement and identification of ASE can be obtained by precise mapping of reads, generated from RNA next generation sequencing (RNA-seq), towards the reference genome of the organism. Mapping bias is a major technical hurdle in ASE studies which arises when we map short RNA-seq reads towards a reference genome. This arises mainly when the reads which carries non-reference alleles is not matching towards the reference genome gives out a lower mapping quality. In this thesis we investigated two proposed methods to reduce mapping bias: a read mapping program called GSNAP, and masking the reference genome with respect to single nucleotide variants. Masking the reference genome removed the mapping bias to a greater degree than GSNAP; however, the masking caused a considerable drop in read coverage. In conclusion, none of the two methods reduced the mapping bias satisfactorily, highlighting the importance to develop new or modified methods for mapping bias reduction.
dc.identifier.urihttps://hdl.handle.net/20.500.12380/179084
dc.language.isoeng
dc.setspec.uppsokPhysicsChemistryMaths
dc.subjectGrundläggande vetenskaper
dc.subjectMatematisk statistik
dc.subjectBasic Sciences
dc.subjectMathematical statistics
dc.titleBenchmarking of read mapping bias in allele specific expression analysis
dc.type.degreeExamensarbete för masterexamensv
dc.type.degreeMaster Thesisen
dc.type.uppsokH
local.programmeBioinformatics and systems biology, MSc
Ladda ner
Original bundle
Visar 1 - 1 av 1
Bild (thumbnail)
Namn:
179084.pdf
Storlek:
1.7 MB
Format:
Adobe Portable Document Format
Beskrivning:
Fulltext
Ladda ner
Samling
Examensarbeten för masterexamen