https://bioinfo.cipf.es/mbb/ 2026-05-29T19:11:35+0200 https://bioinfo.cipf.es/mbb/ https://bioinfo.cipf.es/mbb/lib/tpl/prsnl10/images/favicon.ico text/html 2016-12-12T10:26:12+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/align_handson?rev=1481534772&do=diff Alignment: Practical session #!/bin/bash #move and create directory cd ~/mda12 mkdir -p mapping # index reference time bwa index resources/ref/human_g1k_v37.chr20.fasta time samtools faidx resources/ref/human_g1k_v37.chr20.fasta # align pair 1 time bwa aln -t 1 -l 40 -k 2 resources/ref/human_g1k_v37.chr20.fasta\ resources/data/test_1.fq >\ mapping/test_1.sai # align pair 2 time bwa aln -t 1 -l 40 -k 2 resources/ref/human_g1k_v37.chr20.fasta\ resources/data/test_2.fq >\ mapping/test_… text/html 2018-01-08T14:23:17+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/bierapp_ex1?rev=1515417797&do=diff Data description Working plan We have several candidate profiles of mutations because it is clear the kind of mutation we are searching but sometimes we do not have a specific clues. How many variants do you detect for each scenario? A. Individual filters text/html 2018-01-10T17:46:29+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/bierapp_ex2?rev=1515602789&do=diff Data description Working plan We have several candidate profiles of mutations because it is clear the kind of mutation we are searching but sometimes we do not have a specific clues. How many variants do you detect for each scenario? A. Individual filters text/html 2018-01-10T13:34:57+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/bierapp_ex3?rev=1515587697&do=diff Data description Working plan We have several candidate profiles of mutations because it is clear the kind of mutation we are searching but sometimes we do not have a specific clues. How many variants do you detect for each scenario? A. Individual filters text/html 2018-01-10T14:24:51+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/bierapp_ex4?rev=1515590691&do=diff Data description Working plan We have several candidate profiles of mutations because it is clear the kind of mutation we are searching but sometimes we do not have a specific clues. How many variants do you detect for each scenario? A. Individual filters text/html 2018-01-09T11:43:42+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/bierapp_ex5?rev=1515494622&do=diff Exercise 5 Data description Working plan We have several candidate profiles of mutations to explore: How many variants do you detect for each scenario? A. Individual filters * Recessive heritage * Dominant heritage (mother is affected). text/html 2018-01-09T11:44:09+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/bierapp_ex6?rev=1515494649&do=diff Exercise 6 Data description: cases vs. controls Working plan How many variants do you detect for each scenario? A. Individual filters * Description of variants. How many SNVs, INDELs, MNVs, SVs, CNVs? * Reference for all controls and homozygous variant for all cases. text/html 2017-03-05T17:26:23+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/bierapp_ex7?rev=1488731183&do=diff Exercise 7 Data description Working plan We have several candidate profiles of mutations to explore: How many variants do you detect for each scenario? A. Individual filters * Description of variants. How many SNVs, INDELs, MNVs, SVs, CNVs? * Recessive heritage text/html 2018-01-07T22:02:46+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/bierapp_exercises?rev=1515358966&do=diff Prioritization of variants and genes: BiERapp These exercises show how to analyze exome data for different families or groups. Goal is to detect associated mutations to Mendelian disease. Input data is a set of VCF files. Output analysis will be a selection of candidate variants. text/html 2016-12-12T10:26:12+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/calling_handson?rev=1481534772&do=diff Variant calling and annotation: Practical session #!/bin/bash # Working directory cd ~/mda12/calling # Run program and see options ~/mda12/calling/software/GenomeAnalysisTK-1.4-15-gcd43f01/GenomeAnalysisTK.jar # UnifiedGenotyper ~/mda12/calling/software/GenomeAnalysisTK-1.4-15-gcd43f01/GenomeAnalysisTK.jar\ -T UnifiedGenotyper # Checking the reference head ~/mda12/resources/ref/human_g1k_v37.chr20.fasta head -3000 ~/mda12/resources/ref/human_g1k_v37.chr20.fasta | tail #Checking t… text/html 2016-12-12T10:26:12+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/cipf?rev=1481534772&do=diff The Centro de Investigacion Principe Felipe is a research center focused on regenerative medicine and drug discovery. Visit our web page at: <http://www.cipf.es> [Centro de Investigacion Principe Felipe] text/html 2019-01-10T14:24:52+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/clust_exercise?rev=1547126692&do=diff DATA We have selected the first 200 genes of a breast cancer study with healthy and patient tissues. We want to know if there is any kind of structure in this dataset. Normalized expression set: EXERCISE * Go to Expression -> Unsupervised Analysis Clustering text/html 2016-12-12T10:26:12+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/contact?rev=1481534772&do=diff Contact Course secretary: Laura Galisteo (<lgalisteo@cipf.es>). Computational Genomics Department. Centro de Investigación Príncipe Felipe. Tel: 96 328 96 80, Fax: 96 328 97 01 Address: C/ Eduardo Primo Yúfera, 3 (Junto al Oceanografico) 46012 Valencia, Spain. text/html 2023-01-24T12:53:10+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/csvs_exercises?rev=1674561190&do=diff COLLABORATIVE Spanish Variant Server Estos ejercicios nos muestran cómo obtener información sobre la variabilidad de la población española en diversos escenarios de interés. La herramienta es útil para filtrar polimorfismos y variaciones locales, en el proceso de priorización de genes candidatos para determinadas enfermedades. Desde este enlace text/html 2019-01-10T14:24:31+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/de_exercise?rev=1547126671&do=diff DATA: We have a set of breast cancer patients and a set of healthy samples. We want to know which genes are involved in the development of the disease. For that, we want to perform a differential expression between both groups. The experimental design file includes information about to which class belongs each sample. text/html 2016-12-12T10:26:12+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/deadlines_and_important_dates?rev=1481534772&do=diff Deadlines and important dates: * Course: Wed, 11/07/2012 (All day) - Thu, 12/07/2012 (All day) text/html 2016-12-12T10:26:12+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/equipment?rev=1481534772&do=diff Course Equipment text/html 2021-01-27T13:07:05+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/home?rev=1611749225&do=diff What is WODA? A two day practical course on Web-based Omic Data Analysis. Next generation sequencing data allows the study of biological processes at an unprecedented level of detail. However, transforming such genomic data into valuable biological information is not an easy task. Data analysis is still a major bottleneck for many researchers which are still applying inadequate statistical methods for the interpretation of their genomic results. The aim of this course is to familiarize t… text/html 2016-12-12T10:26:12+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/map?rev=1481534772&do=diff How to arrive See the map to find the CIPF location. text/html 2016-12-12T10:26:12+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/ngs_tutorial?rev=1481534772&do=diff Quality Control Preliminaries Software used in this practical: * FastQC: A quality control tool for high-throughput sequencing data. * cutadapt: A tool to remove adapter sequences from high-throughput sequencing data. File formats explored in this practical text/html 2019-01-10T14:21:53+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/norm_exercise?rev=1547126513&do=diff DATA: We have a dataset in which we have measured the expression profile of two different organs in healthy mice. We have 5 technical replicates per organ: l1-l5 corresponding to Liver, and k1-k5 corresponding to Kidney. Before working with the data set we want to normalize it to correct for possible biases. text/html 2020-01-08T14:05:09+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/panther_exercises?rev=1578488709&do=diff Activities * Functional characterization in genes associated to retinal dystrophies * Functional characterization in genes associated to Charcot-Marie-Tooth disease text/html 2023-01-24T12:45:09+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/program?rev=1674560709&do=diff A. Genomics Francisco García García, fgarcia@cipf.es * General overview of the sessions. Studies of genomic variation. Prioritization of variants and genes. [Introduction]. * CSVS (Collaborative Spanish Variant Server). This database provides information about the variability of the Spanish population. It is very useful for filtering polymorphisms and local variations when prioritizing candidate disease genes. text/html 2019-01-10T14:22:53+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/se_exercise?rev=1547126573&do=diff DATA: We have a set of breast cancer patients and a set of healthy samples. We want to know which functions are involved in the development of the disease. For that, we have performed a differential expression between both groups, and selected the top 50 genes, that is, the 50 genes which are upregulated in patients with breast cancer and have lowest adjusted p.value. text/html 2016-12-12T10:26:12+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/sidebar?rev=1481534772&do=diff COURSE * Home * Program * Teachers * Bioinformatics at CIPF LOGISTICS * Contact * Deadlines and important dates * Map * Accomodation * More courses at CIPF text/html 2022-01-22T17:45:48+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/teachers?rev=1642869948&do=diff Teachers Bioinformatics and Biostatistics Unit. Prince Felipe Research Center: * Marta Hidalgo García, mhidalgo@cipf.es * Francisco García García, fgarcia@cipf.es text/html 2018-01-07T19:33:06+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/mbb/doku.php/team_exercises?rev=1515349986&do=diff TEAM exercises * Activity 1: * * * Activity 2: * *