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# 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

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

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

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.

• 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,...)
• Ferragina Manzini Opportunistic data structures
• FM index
• Repeat resolution
• Spliced mapping

## The project

### Discussion Forum

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

## Proposal

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).

## 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

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Topic attachments
I Attachment Action Size Date Who Comment
pdf 00_Protokoll_main.pdf manage 2 MB 16 Jul 2010 - 12:07 UnknownUser
pdf 1996_BurrowsA_Block-sorting_lossless_Data_Compression.pdf manage 105 K 25 Mar 2010 - 21:40 KnutReinert Original Burrows Wheeler paper
pdf 1Lecture.pdf manage 6 MB 12 May 2010 - 01:05 UnknownUser Slides of lecture 1
pdf 3Lecture.pdf manage 1 MB 16 Jun 2010 - 09:37 UnknownUser
pdf ANNUAL_SYMPOSIUM_ON_FOUNDATIONS_OF_COMPUTER_SCIENCE_2000_FerraginaOpportunistic_Data_Structures_with_Applications.pdf manage 169 K 23 Apr 2010 - 17:58 KnutReinert Ferragina Manzini Opportunistic data structures
pdf Bioinformatics_2002_TammiSeparation_of_nearly_identical_repeats.pdf manage 292 K 09 Jun 2010 - 10:44 KnutReinert Tammi repeat resolution
pdf Bioinformatics_2009_TrapnellTopHat_discovering_splice_junctions_with.pdf manage 333 K 08 Apr 2010 - 11:57 KnutReinert TopHat - Spliced mapping
pdf Genome_Biol_2009_LangmeadUltrafast_and_memory-efficient_alignment_of.pdf manage 538 K 24 Mar 2010 - 15:23 KnutReinert Read Mapping with the BWT
pdf Genome_Research_2002_KentBLAT--the_BLAST-like_alignment_tool.pdf manage 134 K 08 Apr 2010 - 14:08 KnutReinert Blat
pdf Montgomery_et_al._2010_Transcriptome_genetics_using_second_generation_sequencing_in_a_Caucasian_population._Nature.pdf manage 304 K 08 Apr 2010 - 11:47 KnutReinert Transcriptome genetics using second generation sequencing
pdf Nat_Meth_2008_MortazaviMapping_and_quantifying_mammalian_transcriptomes.pdf manage 1 MB 24 Mar 2010 - 07:40 KnutReinert Mortzavi RNA-Seq
pdf Proceedings_of_the_fifth_annual_international_conference_on_Computational_biology_2001_KececiogluSeparating_repeats_in_DNA_sequence.pdf manage 256 K 09 Jun 2010 - 10:45 KnutReinert Kececioglu repeat separation
pdf Proceedings_of_the_twelfth_annual_ACM-SIAM_symposium_on__2001_FerraginaAn_experimental_study_of_an.pdf manage 767 K 25 Apr 2010 - 20:38 KnutReinert FM index
pdf Proposal.pdf manage 1 MB 11 May 2010 - 22:28 UnknownUser Proposal
pdf a1_2-maniscalco.pdf manage 247 K 24 Mar 2010 - 15:25 KnutReinert Suffix array construction overview and fast algorithm
pdf enhanced-suffix-array.pdf manage 147 K 24 Mar 2010 - 15:27 KnutReinert Enhanced suffix array script
pdf exercise3.pdf manage 68 K 16 Jun 2010 - 09:41 UnknownUser Exercise of lecture 3
pdf filtering.pdf manage 1 MB 24 Mar 2010 - 15:22 KnutReinert Lecture script about filtering
pdf flux_supplementary.pdf manage 2 MB 08 Apr 2010 - 11:47 KnutReinert Transcriptome genetics using second generation sequencing suppl.
pdf myers-bitvector-verification.pdf manage 206 K 24 Mar 2010 - 15:24 KnutReinert Bit-parallel verification
pdf presentation.pdf manage 219 K 22 Jul 2010 - 14:28 UnknownUser Project presentation (Corinna Blasse)
pdf repeat-separation.pdf manage 314 K 24 Mar 2010 - 15:27 KnutReinert Repeat separation script
pdf rnaseq_exercise2.pdf manage 49 K 27 May 2010 - 14:01 UnknownUser Exercise to lecture 2 (this is the corrected version)
pdf rnaseq_lecture2.pdf manage 1 MB 27 May 2010 - 14:00 UnknownUser Slides to the second lecture
pdf suffix-array.pdf manage 289 K 24 Mar 2010 - 15:26 KnutReinert Suffix array script
Topic revision: r51 - 22 Jul 2010, cblasse