Deletion log

Below is a list of the most recent deletions.

• 13:17, 29 May 2026 Haars0011 talk contribs deleted page Genetics and Genomics (content was: "The sphere of activity of genetics and genomics involves identifying the role of genetic factors in the functioning of farm animals and companion animals, as well as designing optimal breeding schemes for selection. The Animal Breeding & Genomics Centre (ABGC) works closely with the Department of Animal Sciences of Wageningen University. The ABGC has three key expertise are...", and the only contributor was "Hjmegens" (talk))
• 13:16, 29 May 2026 Haars0011 talk contribs deleted page Geneid 1.4.4 (content was: "[http://genome.crg.es/software/geneid/ geneid] is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## geneid 1.4.4 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds geneid v1.4.4 to your environment" } module-whatis "Adds gen...")
• 13:16, 29 May 2026 Haars0011 talk contribs deleted page Fastq (content was: "'''FASTQ format''' is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are encoded with a single ASCII character for brevity. It was originally developed at the Wellcome Trust Sanger Institute to bundle a FASTA sequence and its quality data, but has recently become the ''de facto'' standard for storing the output o...")
• 13:16, 29 May 2026 Haars0011 talk contribs deleted page Exonerate 2.2.0 (content was: "[https://www.ebi.ac.uk/~guy/exonerate/ Exonerate] is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <source lang='tcl'> #%Module1.0#######...", and the only contributor was "Megen002" (talk))
• 13:16, 29 May 2026 Haars0011 talk contribs deleted page Cufflinks (content was: "'''[http://cufflinks.cbcb.umd.edu Cufflinks]''' assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support...", and the only contributor was "Megen002" (talk))
• 13:16, 29 May 2026 Haars0011 talk contribs deleted page Computer cluster (content was: "The HPC infrastructure at the Animal Breeding and Genomics Centre is currently in a transition phase. Over the past years the main infrastructure consisted of the Lx6 and Lx7 compute nodes. As of December 2013 the new B4F cluster has become online is expected to replace the old infrastructure early 2014. The Lx6 and Lx7 comp...", and the only contributor was "Hjmegens" (talk))
• 13:15, 29 May 2026 Haars0011 talk contribs deleted page Cegma 2.4 (content was: "CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome. The strategy relies on a simple fact: some highly conserved proteins are encoded in essentially all eukaryotic genomes. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## cegma 2.4 mod...")
• 13:15, 29 May 2026 Haars0011 talk contribs deleted page Canu (content was: "Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). Canu is a hierarchical assembly pipeline which runs in four steps: * Detect overlaps in high-noise sequences using MHAP * Generate corrected sequence consensus * Trim corrected sequences * Assemble trimmed corrected sequen...", and the only contributor was "Dawes001" (talk))
• 13:13, 29 May 2026 Haars0011 talk contribs deleted page Bwa 7.5 (content was: "[http://en.wikipedia.org/wiki/Burrows-Wheeler_Aligner#Short-Read_Sequence_Alignment BWA] is a short read aligner designed by Heng Li and currently the most widely used aligner for re-sequencing analysis. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <source lang='tcl'> #%Module1.0#########################################...", and the only contributor was "Megen002" (talk))
• 13:12, 29 May 2026 Haars0011 talk contribs deleted page Bwa 5.9 (content was: "[http://en.wikipedia.org/wiki/Burrows-Wheeler_Aligner#Short-Read_Sequence_Alignment BWA] is a short read aligner designed by Heng Li and currently the most widely used aligner for re-sequencing analysis. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <source lang='tcl'> #%Module1.0#########################################...", and the only contributor was "Megen002" (talk))
• 13:12, 29 May 2026 Haars0011 talk contribs deleted page Bowtie2 v2.2.1 (content was: " '''[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]''' is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an...", and the only contributor was "Megen002" (talk))
• 13:12, 29 May 2026 Haars0011 talk contribs deleted page Bowtie1 v1.0.0 (content was: "'''[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie]''' is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB f...", and the only contributor was "Megen002" (talk))
• 13:12, 29 May 2026 Haars0011 talk contribs deleted page Blat v35 (content was: "'''[http://en.wikipedia.org/wiki/BLAT_(bioinformatics) BLAT]''' (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the Human Genome. == Module file == The module file can be found in this location: /cm/shared...", and the only contributor was "Megen002" (talk))
• 13:12, 29 May 2026 Haars0011 talk contribs deleted page Bioinformatics topics at ABG Chairgroup (content was: "This page contains a list of research topics. * Pig ERC project * Porcine HapMap project", and the only contributor was "Hjmegens" (talk))
• 13:11, 29 May 2026 Haars0011 talk contribs deleted page DE expression (content was: "=== Typical commands used for doing a DE expression study using Tophat (including Bowtie2 as aligner), Stringtie and Cuffdiff === Author: Martijn Derks * Samtools, Trimmomatic, Tophat, Bowtie2, Stringtie, Cufflinks need to be in PATH. * Use case in wintermoth. 12 samples (1 Egg, 1 Caterpillar, 3x3 Pupa, 1 Moth). ===Trim sequences for quality and adapters=== <source lang...", and the only contributor was "Derks047" (talk))
• 13:11, 29 May 2026 Haars0011 talk contribs deleted page Issues asreml (content was: "Issues with ASReml on the HPC and possible solutions == Issue with the environment variable DISPLAY == '''Issue''' Some terminals for Windows (e.g., MobaXterm) set the environment variable DISPLAY to a specific value. This can cause issues with (some versions of) ASReml. '''Solution 1''' If you don't need a X11 server, you can disable it. '''Solution 2''' You can a...", and the only contributor was "Vande018" (talk))
• 13:11, 29 May 2026 Haars0011 talk contribs deleted page Variant annotation tutorial (content was: "Code and tutorials for CIHEAM course. Variation annotation and function prediction sessions == Variant annotation == make a new folder to work in, and go there: <source lang='bash'> mkdir annotation_session cd annotation_session </source> Create an Env.Var. to the communal session directory that holds some of the files you need: <source lang='bash'> SESSIONDIR=/home/for...", and the only contributor was "Megen002" (talk))
• 13:10, 29 May 2026 Haars0011 talk contribs deleted page RNA-seq analysis (content was: " === Typical commands used for analyzing RNA-seq with Tophat (including Bowtie2 as aligner).=== * Examples are RNA-seq (stranded) from pig aligned against the pig reference genome (''S. scrofa'' - 10.2) * Tophat, Bowtie2, Picard and GATK need to be in PATH or loaded as modules (e.g.: module load SHARED/bowtie/2-2.2.1; module load SHARED/tophat/2.0.11) * Bowtie2 index (made with bowtie2_build) of reference genome (need only to be made ones) * PCR duplicates removed with Picar...")
• 13:10, 29 May 2026 Haars0011 talk contribs deleted page Calculate corrected theta from resequencing data (content was: "This procedure will estimate theta (nucleotide diversity) based on re-sequencing data. The method is describe in [http://www.biomedcentral.com/1471-2164/14/148 Esteve-Codina et al.] <source lang ='bash'> #!/bin/bash #SBATCH --time=10000 #SBATCH --mem=4000 #SBATCH --ntasks=1 #SBATCH --nodes=1 #SBATCH --constraint=4gpercpu #SBATCH --output=output_%j.txt #SBATCH --error=error_output_%j.txt #SBATCH --job-name=ngstheta module load samtools/0.1.19 VAR=`gunzip -c /lustre/nobackup/WU...")
• 13:10, 29 May 2026 Haars0011 talk contribs deleted page Extract noncall snps from soy (content was: "== Extract the SNPs that are not called in Soy == From the <code>.ped</code> file, only the soy samples were extracted, and call rate calculated like this: <source lang='bash'> ./plink --file soy --out soy --missing-genotype N --freq --noweb </source> The output data looks like this: CHR SNP A1 A2 MAF NCHROBS 1 MARC0044150 0 0...", and the only contributor was "Megen002" (talk))
• 13:10, 29 May 2026 Haars0011 talk contribs deleted page Command line tricks for manipulating fastq (content was: "== Extracting a sequence based on read name == <source lang='bash'> gunzip -c reads.fq.gz | sed -n '/readname/,+3 p' </source> == From BAM/SAM to fastq == <source lang='bash'> samtools view bamfile.bam | grep -v '^@' | awk '{print "@"$1"\n"$10"\n+\n"$11}' </source> == From fastq to fasta == <source lang='bash'> gunzip -c fastqfile.fq.gz | sed 's/^@/>/' | awk '{print;get...", and the only contributor was "Megen002" (talk))
• 13:09, 29 May 2026 Haars0011 talk contribs deleted page Short read mapping pipeline pig (content was: "The latest short-read mapping pipeline for the pig project is based on a Python3 script that creates a shell script that can subsequently be executed from the command line or submitted to the cluster using SLURM. The latest version of the Python3 script can be found at [https://github.com/hjmegens/NGStools/blob/master/ABGC_mapping_v2.py GitHub]. The script requires to be executed using python3. == Prerequisites == === Data sources === * path to sequence archives...")
• 13:08, 29 May 2026 Haars0011 talk contribs deleted page Making slices from BAM files (content was: "This article describes how to automate the creation of slices from a collection of BAM files. This procedure assumes that all BAM files are together in a single folder. == Variable that points to the collection of bam files == First, make a variable BAMDIR that holds the path to the BAM files: <source lang='bash'> BAMDIR='/shared/Sus/BAM_files_hjm_newbuild10_2/' </source>...", and the only contributor was "Hjmegens" (talk))
• 13:08, 29 May 2026 Haars0011 talk contribs deleted page Convert fastq to fasta (content was: "Converting fasq to fasta can sometimes be useful. Here a simple perl script is described that can do this. The script works on a stream, and will output to STDOUT. Optional is filtering for reads that have a certain minimum length Example for invoking the script, assuming the script is named fastq_to_fasta.pl: <source lang='bash'> gunzip -c fastqfile.fq.gz | perl fastq_to_...", and the only contributor was "Hjmegens" (talk))
• 13:07, 29 May 2026 Haars0011 talk contribs deleted page Mapping reads with Mosaik (content was: "Within the Pig ERC project we have several mapping strategies. This article describes the mapping procedure using Mosaik for paired-end mapping to the reference assembly. == Prerequisites == === input reads === The mapping procedure requires paired end reads in fastq format. For the current procedure quality-trimmed reads are used. Forward and reverse reads should be in tw...", and the only contributor was "Hjmegens" (talk))
• 13:07, 29 May 2026 Haars0011 talk contribs deleted page Bioinformatics protocols ABG Chairgroup (content was: "This page is intended as a portal to pages concerning best practices, workflows and pipelines, and other protocols (including scripts). == A list of tutorials, workflows, and recipes == * Mapping Illumina GA2/HiSeq reads to the Sus scrofa genome assembly * A Perl script to convert fastq to fasta file format * Setup Printers on Ubuntu Machines * Mapping Pair-end reads with Stampy * making_slices_from_BAM_fil...")
• 13:07, 29 May 2026 Haars0011 talk contribs deleted page Bedtools2.18 (content was: "Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect t...")
• 13:07, 29 May 2026 Haars0011 talk contribs deleted page BLAST (content was: "'''B'''asic '''L'''ocal '''A'''lignment '''S'''earch '''T'''ool, or '''[http://en.wikipedia.org/wiki/BLAST BLAST]''', is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of s...", and the only contributor was "Megen002" (talk))
• 13:07, 29 May 2026 Haars0011 talk contribs deleted page BCPlatforms (content was: "{| class=wikitable | Issue || Originating contact person || Person handling issue || Comments |- | Test Issue || Me || You ja dat zal wel een problem kunnen zijn . zeker als ik het veel tekst geef || A test issue. |- | Test Issue 2 || |}")
• 13:06, 29 May 2026 Haars0011 talk contribs deleted page BCM on Anunna (content was: "Computing clusters are usually managed by [http://en.wikipedia.org/wiki/Cluster_manager cluster managing software]. Anunna uses the cluster management sofware from [http://www.brightcomputing.com Bright ]. BCM is currently is a popular choice for compute clusters of any size, including some very large ones. Bright is a spin-off from [http://www.clustervision.com ClusterVision], the company that aided in implementing the cluster. Furthermore, ClusterVision and [http://www.cluste...")
• 13:06, 29 May 2026 Haars0011 talk contribs deleted page BCData (content was: "This page contains information about BCData", and the only contributor was "Lith010" (talk))
• 13:05, 29 May 2026 Haars0011 talk contribs deleted page Augustus 2.7 (content was: ""AUGUSTUS is a gene prediction program for eukaryotes genomic sequences. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments." == Module file == The module file can be...", and the only contributor was "Megen002" (talk))
• 13:05, 29 May 2026 Haars0011 talk contribs deleted page Assembly & Annotation (content was: "=== Protocol with typical commands used for de novo assembly and annotation === ''Author:'' Martijn Derks ''All script referred to in this protocol can be found here:'' /home/WUR/derks047/BifDev/derks047 * Software * Preprocessing * Assembly * Assembly validation * Annotation * Submission * Visualization === Software === List of tools described in this protocol [http:...", and the only contributor was "Derks047" (talk))
• 13:05, 29 May 2026 Haars0011 talk contribs deleted page Assemble mitochondrial genomes from short read data (content was: "A simple procedure for assembling mitochondrial genomes based on whole-genome re-sequencing data. The first step is to extract reads from the sequence library based on a closely related entirely assembled genome (e.g., for pig, the MT genome as present in the genome build, but could also be of a related species). The genome is then assembled using SOAPdenovo. * a reference genome of a closely related population or species. * a bowtie2 index (make with bowtie2_build) * a blasta...")
• 13:05, 29 May 2026 Haars0011 talk contribs deleted page Animal Breeding and Genetics (content was: "The [http://www.abg.wur.nl/UK/ Animal Breeding and Genetics] chair group provides education and generates knowledge on the role and sustainable use of genetic variation in animals. The Animal Breeding and Genetics group contributes to our quality of life by providing knowledge to support the adequate supply of safe and healthy food of animal origin, and to enhance the healt...", and the only contributor was "Hjmegens" (talk))
• 13:05, 29 May 2026 Haars0011 talk contribs deleted page Allpathslg 51910 (content was: " '''[http://www.broadinstitute.org/software/allpaths-lg/blog/ ALLPATHS-LG]''' is a popular genome assembler. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## maker ALLPATHS-LG (51910 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds ALLPATHS-LG (51910) to your environment" } module-whatis "Adds ALLPATHS-LG (51910) to...")
• 13:04, 29 May 2026 Haars0011 talk contribs deleted page Allpathslg 48961 (content was: " '''[http://www.broadinstitute.org/software/allpaths-lg/blog/ ALLPATHS-LG]''' is a popular genome assembler. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## maker ALLPATHS-LG (48961 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds ALLPATHS-LG (48961) to your environment" } module-whatis "Adds ALLPATHS-LG (48961) to...")
• 13:03, 29 May 2026 Haars0011 talk contribs deleted page About ABGC (content was: "The Animal Breeding and Genomics Centre is a merger of the Animal Breeding & Genetics chair group, of the [http://www.wageningenuniversity.nl/UK/about/organisation/Chair%20groups/animal/ Animal Sciences Group], Wageningen University, and the Genetics and Genomics cluster of the WUR [http://www.livestockresearch.wur.nl/UK/ Livestock Research] Centre. The ABGC has three key...", and the only contributor was "Hjmegens" (talk))
• 13:03, 29 May 2026 Haars0011 talk contribs deleted page ANGSD 0.614 (content was: "[http://popgen.dk/wiki/index.php/ANGSD ANGSD] ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium dep...", and the only contributor was "Herre011" (talk))
• 13:03, 29 May 2026 Haars0011 talk contribs deleted page ABGSA (content was: "== Rationale of the ABGSA == == Description of the layout == == Metadata database == Metadatabase name is ABGSAschema +-----------------------+ | Tables_in_ABGSAschema | +-----------------------+ | ABGSAschema_main | | filesize | | fqfile_attributes | | gc_cont | +-----------------------+ The most recent mysqldump file...", and the only contributor was "Hjmegens" (talk))
• 13:02, 29 May 2026 Haars0011 talk contribs deleted page ABGC secretariat (content was: "== Animal Breeding and Genetics Chair Group == <pre> Visiting Address Zodiac building number 122 De Elst 1 6708 WD, Wageningen Telefax: +31 317 483929 office.abg@wur.nl </pre> == Genetics and Genomics Research Cluster == ===Headquarters Lelystad:=== <pre> Visiting address Edelhertweg 15 8219 PH Lelystad Postal address P.O. Box 65 8200 AB Lelystad tel: +31 320 238 238 fa...", and the only contributor was "Hjmegens" (talk))
• 13:02, 29 May 2026 Haars0011 talk contribs deleted page ABGC lab (content was: "* protocols", and the only contributor was "Hjmegens" (talk))
• 13:02, 29 May 2026 Haars0011 talk contribs deleted page ABGC bioinformatics (content was: "The ABGC has several shared bioinformatics facilities. == Bioinformatics at the Animal Breeding and Genetics chairgroup == * Monday Genome Meeting * Bioinformatics: topics * best practices, tips and workflows == Bioinformatics at the Genetics and Genom...", and the only contributor was "Hjmegens" (talk))
• 13:01, 29 May 2026 Haars0011 talk contribs deleted page 1000Bulls mapping pipeline at ABGC (content was: "The 1000 Bulls mapping pipeline as currently implemented at ABGC is an extension of a generic pipeline developed for pig at ABGC. Modifications include use of bwa 5.9 in stead of later versions, as per the requirements of the 1000 Bulls consortium. Furthermore, the script will automate setting metadata in the BAM files such as including the official 1000 Bulls Ids of the individual cows. Another modification is the use of an sqlite-based database that holds some the metadata re...")
• 13:00, 29 May 2026 Haars0011 talk contribs deleted page AsAn (content before blanking was: "=== Protocol with typical commands used for de novo assembly and annotation === * Preprocessing * Assembly * Annotation * Submission * Visualization === Preprocessing === === Assembly === === Annotation === === Functional annotation === === Submission === === Other types of analysis ===")
• 12:50, 29 May 2026 Haars0011 talk contribs deleted page Convert between MediaWiki and other formats (content was: "There are various programs that can convert to and from MediaWiki format, as used in this Wiki, and other formats. This page lists some of them and provides explanation of how to use them. == Pandoc == [http://johnmacfarlane.net/pandoc/demos.html Pandoc] is an open source tool that can convert between different markup styles and languages. There is a [http://johnmacfarlane.net/pandoc/try/ web version of Pandoc] but that seems limited to small documents only. There's also a C...")
• 12:48, 29 May 2026 Haars0011 talk contribs deleted page New page (content was: "Now here is some stuff", and the only contributor was "Megen002" (talk))
• 11:11, 11 July 2017 Dawes001 talk contribs deleted page Template:Warning (Author request)
• 19:43, 4 March 2012 Hjmegens talk contribs deleted page File:Bioinformatics-infra.gif (Deleted old revision 20120304194236!Bioinformatics-infra.gif: updated picture)
• 08:53, 25 November 2011 Hjmegens talk contribs deleted page File:Logo.gif