User: Ylebras

NGS : Tuto SNP detection workflow single end (1)

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Generate pileup, Unify Genotypers and create a VCF file from FastQ files of two individuals

Created: 2014-03-05 | Last updated: 2014-06-10

Credits: Ylebras

NGS RAD : Population Genomics on RAD data ... (1)

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Analyse clean population fastQ files (coming from Stacks : Process Radtag tool for example) without a reference genome and population information

Created: 2014-03-05

NGS RAD : Population Genomics on RAD data ... (1)

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Analyse clean population SAM files (coming from alignment of FastQ from Stacks : Process Radtag tool for example) with a reference genome and population information

Created: 2014-03-05 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Group and filter mapped reads (1)

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Filter and group reads from a mapping Bam file

Created: 2014-03-05 | Last updated: 2014-06-10

Credits: Ylebras

Tuto Galaxy 2013 : GenOuest, from Fasta to... (1)

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Create a tree from a multifastafile using ClustalW, PhylipDNAdist, PhylipNeighbor, PhylipDrawtree and Treevector, for interactive visualization in Phyloviz or static on pdf or svg format. Then, using the same multifasta file, handling sequences file, use blast on a reference genome and filter results to have sequences with more than 90% identity.

Created: 2014-03-05 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Tuto SNP detection workflow single end (1)

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Generate pileup, Unify Genotypers and create a VCF file from FastQ files of two individuals

Created: 2014-03-04 | Last updated: 2014-06-10

Credits: Ylebras

Transcritomics : eQTL after data extractio... (1)

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Format raw files from Feature extraction output (Agilent array matrix file) to have individual in columns and genes in rows

Created: 2014-03-04 | Last updated: 2014-06-10

Credits: Ylebras

NGS : RNAseq workflow part 1 from Tophat t... (1)

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Remove duplicates from Tophat BAM output files and filter

Created: 2014-03-04 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Mini assembly from FastQ files using... (1)

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Assemble FastQ reads with minia

Created: 2014-02-28 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Filter contamination in raw reads by ID (1)

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Filter FastQ sequences by ID

Created: 2014-02-28 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Bowtie2 using built-in genome to dep... (1)

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Reads mapping using a built-in genome from your history, then generate pileup, base coverage, depth of coverage and summary statistics

Created: 2014-02-28 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Bowtie2 with a genome in fasta forma... (1)

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Reads mapping using a reference genome in fasta format from your history, then generate pileup, base coverage, depth of coverage and summary statistics

Created: 2014-02-28 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Coverage determination and visualiza... (1)

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From a BAM file and a reference genome fasta file, calculate the depth of coverage and generate pileup, interval, Base coverage as Summary statistics

Created: 2014-02-28 | Last updated: 2014-06-10

Credits: Ylebras

NGS : flanking SNP regions (1)

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Flank SNP regions using interval format file and a fasta reference file

Created: 2014-02-28 | Last updated: 2014-06-10

Credits: Ylebras

Population genomics : From Blast xml forma... (1)

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Parse Blast XML results to obtain species specifics sequences

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

NGS : RNA-seq differential expression anal... (1)

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Analyse paired-end RNA-seq reads of 2 different individuals with FastQC, Tophat2, Cufflinks and Cuffdiff using a reference annotation in gtf format

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Filtrer fastq reads with N (1)

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Filter FastQ file and delete sequences with N

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

Population genomics : Structure and CLUMPP (1)

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Population genomics analysis using Structure and Clumpp to cluster data

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

NGS : FastQ Quality check and FastQ manipu... (1)

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Taking FastQ reads, apply FastQ groomer on sequences and generate Quality reports (FastQC, Summary statistics, boxplots) before and after filter

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

Tuto Galaxy 2013 : CPB2012 - BasicProtocol... (1)

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Workflow used when applying the CPB2012 Basic Protocol 1 tutorial from Galaxy team. It permits to filter Exons with the most SNP density.

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

NGS : Pair reads assembly with Velvet Work... (1)

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Paired-end reads assembly after fastQ groomer using a Migale (France INRA core facility https://migale.jouy.inra.fr/) modified version of Velvet tool suite descriptors

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

Tuto Galaxy 2013 : CPB2012 - BasicProtocol... (1)

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Workflow used when applying the CPB2012 Basic Protocol 3 tutorial from Galaxy team. It calls peaks for ChIP-seq data using MACS14.

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras