Difference between revisions of "INF-BIOX120 H13 course material"
(→Quality control) |
|||
(15 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
+ | == Introduction == | ||
+ | |||
+ | [[Media:SequencingTech%26Applic_INF-BIO_2013.pdf|Introduction to High-throughput sequencing technologies and applications]] (pdf)<br> | ||
+ | |||
== File formats == | == File formats == | ||
[[Media:HTS_Course_file_formats.pdf|HTS_Course_file_formats]] (pdf)<br>[[Media:HTS_Course_file_formats_exercises.pdf|HTS_Course_file_formats_exercises]] (pdf)<br> | [[Media:HTS_Course_file_formats.pdf|HTS_Course_file_formats]] (pdf)<br>[[Media:HTS_Course_file_formats_exercises.pdf|HTS_Course_file_formats_exercises]] (pdf)<br> | ||
− | == Quality control == | + | == Quality control == |
+ | |||
+ | [https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly/blob/master/practicals/00_Read_QC.md Read QC practical] (webpage) | ||
+ | |||
+ | == miRNA == | ||
+ | |||
+ | [https://wiki.uio.no/projects/clsi/images/0/0f/MicroRNA_theory.pdf microRNA_theory] (pdf)<br> [https://wiki.uio.no/projects/clsi/images/f/fb/MicroRNA_analysis.pdf microRNA_analysis] (pdf)<br> [http://www.biomedcentral.com/1471-2164/13/320 Baboon_miRNA] (link to article)<br> [https://wiki.uio.no/projects/clsi/images/7/74/EdgeR.pdf edgeR] (pdf)<br> [https://wiki.uio.no/projects/clsi/images/9/99/MiRNA_analysis_infbio_practicals.pdf miRNA_analysis_infbio_practicals] (pdf) | ||
+ | |||
+ | == RNAseq == | ||
+ | |||
+ | [https://wiki.uio.no/projects/clsi/images/d/da/RNAseq_introduction180913.pdf RNAseq_introduction180913] (pdf)<br>[https://wiki.uio.no/projects/clsi/images/2/26/Introduction_Differential_Expression.pdf Introduction Differential Expression] (pdf)<br>[https://wiki.uio.no/projects/clsi/images/4/42/INF-BIOx120_RNASeq_Analysis.pdf INF-BIOx120 RNASeq Analysis] (pdf)<br>[https://wiki.uio.no/projects/clsi/images/e/e0/Commands.txt commands.txt] | ||
+ | |||
+ | == Variant calling == | ||
+ | |||
+ | [https://wiki.uio.no/projects/clsi/images/8/80/VariantCallingCourse_sept2013_Part1.pdf variantCallingCourse_sept2013_Part1](pdf) | ||
+ | |||
+ | [https://wiki.uio.no/projects/clsi/images/3/3d/VariantCallingCourse_sept2013_Part2.pdf variantCallingCourse_sept2013_Part2] (pdf) | ||
+ | |||
+ | == ''De novo'' assembly == | ||
− | [https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly/ | + | See this github repo: [https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly] |
− | == | + | == Statistical genomics == |
− | + | [https://wiki.uio.no/projects/clsi/images/b/b6/StatisticalGenomics_part_1.pdf StatisticalGenomics_part_1] (pdf)<br>[https://wiki.uio.no/projects/clsi/images/8/87/StatisticalGenomics_part_3.pdf StatisticalGenomics_part_3] (pdf)<br>[https://wiki.uio.no/projects/clsi/images/4/41/StatisticalGenomics_part_4.pdf StatisticalGenomics_part_4] (pdf)<br>[https://wiki.uio.no/projects/clsi/images/3/31/Pres_ChoiceOfWaysOfInteractingWithBioinformatics_v2.pdf ChoiceOfWaysOfInteractingWithBioinformatics] (pdf)<br> |
Latest revision as of 12:51, 7 October 2013
Contents
Introduction
Introduction to High-throughput sequencing technologies and applications (pdf)
File formats
HTS_Course_file_formats (pdf)
HTS_Course_file_formats_exercises (pdf)
Quality control
Read QC practical (webpage)
miRNA
microRNA_theory (pdf)
microRNA_analysis (pdf)
Baboon_miRNA (link to article)
edgeR (pdf)
miRNA_analysis_infbio_practicals (pdf)
RNAseq
RNAseq_introduction180913 (pdf)
Introduction Differential Expression (pdf)
INF-BIOx120 RNASeq Analysis (pdf)
commands.txt
Variant calling
variantCallingCourse_sept2013_Part1(pdf)
variantCallingCourse_sept2013_Part2 (pdf)
De novo assembly
See this github repo: https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly
Statistical genomics
StatisticalGenomics_part_1 (pdf)
StatisticalGenomics_part_3 (pdf)
StatisticalGenomics_part_4 (pdf)
ChoiceOfWaysOfInteractingWithBioinformatics (pdf)