Page RnaSeqP4

This is the project page of the RNA-Seq group.

Students

Mail an alle Gruppenmitglieder: AA2010SS-RNASeq bei lists.spline.de

Name	email
Corinna Blasse	cblasse@mi.fu-berlin.de
Nicolas Balcazar	balcazar@mi.fu-berlin.de
An Duc Dang	an.duc.dang@fu-berlin.de
Sebastian Thieme	thieme@mi.fu-berlin.de
Hannes Hauswedell	hauswedell@mi.fu-berlin.de

Literature

Initial reading (this should be read by all)

In this paper you have a fairly complete description of the RNA-Seq pipeline.

Also, for the core lecture you should read the following:

• Lecture script about filtering
• Read Mapping with the BWT
• Bit-parallel verification

In the further reading section I will give additional reading for some algorithmic problems connected with RNA-Seq. The section contains material that is related to the algorithmic problems occurring in the RNA-Seq analysis and can serve as a basis for your 2 additional lectures.

Further reading

• Suffix arrays, enhanced suffix arrays, and help tables (possible lectures could comprise, suffix array construction, a lecture how enhanced suffix arrays can replace suffix trees,...)
  • Original Burrows Wheeler paper
• Ferragina Manzini Opportunistic data structures
• FM index
  • Suffix array construction overview and fast algorithm construction algorithm
  • Suffix array script
  • Enhanced suffix array script
  • Michael Sammeth RNA-Seq tool
  • Supplement to Michael Sammeths paper
• Repeat resolution
  • Repeat separation script
• Spliced mapping
  • TopHat spliced mapping
  • BLAT--the_BLAST-like_alignment_tool.pdf

The project

Discussion Forum

Please use this space to interface between each other and with the instructors

Proposal

• Slides of the proposal

1. Lecture: Read mapping

• Slides of lecture 1 (13 May 2010 5:26p.m.)

Topics: Bowtie → Suffix Arrays, BWT, EXACTMATCH, Backtracking

Excercise

Task 1: Compute the BWT for S=ACGCACGTACGG. Apply the exact match algorithm of the lecture to find the number of occurrences of the Pattern P=ACG. In the lecture we will learn how to also find the positions in the text and extend the example.

Task 2: Compute all matches with exactly one mismatch of the Pattern P=AGG using the backtracking algorithm of the lecture. (It will be given on Wednesday, nevertheless prepare ALL for it).

2. Lecture

• Slides of lecture 2
• Exercise of lecture 2 (corrected)

3. Lecture

• Slides of lecture 3 (corrected)
• Exercise of lecture 3

Script

• lecture script (16.07.2010)

Analysis/Programming Projects

Quality assessment of read mapper(s) concerning multireads (An Duc Dang, David Weese)

In order to analyse how read mapper(s) deal with multireads I will pick repeats of a well annotated genome to synthesize mutated repeats and insert those into the genome. The outcome of the read mapper will be compared to the set of the simulated reads. Here you find more details.

Detecting viral integration sites (Corinna Blasse, Instructor: Birte Kehr)

In this project we will use the local mapping algorithms of SeqAn to map colorspace SOLID reads to the human and a viral genome in order to find integration sites of the virus in the human. Here you find the details.

presentation.pdf: Project presentation (Corinna Blasse)

Comparison of Bowtie and bwa (Sebastian Thieme und Hannes Hauswedell, Instructor: Manuel Holtgrewe)

In this project we want to investigate the difference of the two mapping tools bowtie and bwa. Here you find the details.

Effect of read length on the sensitivity of detecting spliced reads (Nicolas Balcazar, Instructor: David Weese)

In this project I want to investigate the relation of increasing read length of mRNA reads versus the amount of reads that cannot be mapped by read mappers that do not compute a spliced alignment. Here

• Nat_Meth_2008_MortazaviMapping_and_quantifying_mammalian_transcriptomes.pdf: Mortzavi RNA-Seq
• filtering.pdf: Lecture script about filtering
• Genome_Biol_2009_LangmeadUltrafast_and_memory-efficient_alignment_of.pdf: Read Mapping with the BWT
• myers-bitvector-verification.pdf: Bit-parallel verification
• a1_2-maniscalco.pdf: Suffix array construction overview and fast algorithm
• suffix-array.pdf: Suffix array script
• enhanced-suffix-array.pdf: Enhanced suffix array script
• repeat-separation.pdf: Repeat separation script
• 1996_BurrowsA_Block-sorting_lossless_Data_Compression.pdf: Original Burrows Wheeler paper
• Sammeth RNA-Seq.pdf: Transcriptome genetics using second generation sequencing
• Sammeth_supplementary.pdf: Transcriptome genetics using second generation sequencing suppl.
• TopHat.pdf: TopHat - Spliced mapping
• Genome_Research_2002_KentBLAT--the_BLAST-like_alignment_tool.pdf: Blat
• Ferragina Focs.pdf: Ferragina Manzini Opportunistic data structures
• Proceedings_of_the_twelfth_annual_ACM-SIAM_symposium_on__2001_FerraginaAn_experimental_study_of_an.pdf: FM index

• rnaseq_lecture2.pdf: Slides to the second lecture

• rnaseq_exercise2.pdf: Exercise to lecture 2 (this is the corrected version)

• Bioinformatics_2002_TammiSeparation_of_nearly_identical_repeats.pdf: Tammi repeat resolution

• Proceedings_of_the_fifth_annual_international_conference_on_Computational_biology_2001_KececiogluSeparating_repeats_in_DNA_sequence.pdf: Kececioglu repeat separation

• exercise.pdf: Exercise 3

• 3Lecture.pdf: 3Lecture.pdf

• exercise.pdf: Exercise 3

• exercise3.pdf: Exercise of lecture 3