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Getting Started with Taverna - an NGS tutorial

Created: 2012-05-23 14:53:24 | Last updated: 2012-05-30 08:48:19

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 83 times | Downloaded: 85 times

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Biosurfactants and Biodegradation

Unique name: biosurf
Created: Wednesday 28 October 2015 11:25:54 (UTC)

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The NOTCH2 workflow (1)

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Analysis of the exome sequencing data for the following article: Nat Genet. 2011 Mar 6;43(4):306-8. Truncating mutations in the last exon of NOTCH2 cause a rare skeletal disorder with osteoporosis. Isidor B, Lindenbaum P, Pichon O, Bézieau S, Dina C, Jacquemont S, Martin-Coignard D, Thauvin-Robinet C, Le Merrer M, Mandel JL, David A, Faivre L, Cormier-Daire V, Redon R, Le Caignec C. using knime4bio

Created: 2011-09-06 | Last updated: 2011-09-06

Credits: PL

Define Associated Regions and Genes (2)

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Defines regions and genes from associated SNPs A JAVA MySQL connector is required to run the workflow and must be placed in the $TAVERNA_HOME/lib directory.

Created: 2012-02-08 | Last updated: 2012-05-09

Credits: Paul martin

Perform QC on FastQ data (1)

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 This Galaxy pipeline performs quality control analyses on FastQ data. A report is generated which provides various measures of the quality of the sequence reads.

Created: 2012-06-14 | Last updated: 2012-06-14

Advanced FastQ manipulation (1)

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 This Galaxy workflow performs advanced FastQ manipulation as demonstrated by the screencast at http://screencast.g2.bx.psu.edu/quickie_14_fastq_adv/flow.html. Given a FastQ set of data, it will be transformed using the tools, Groomer, Filter FastQ, FastQ Trimmer, Manipulate FastQ before it is finally converted into FASTA format.

Created: 2012-06-14 | Last updated: 2012-06-14

BowtieToPileup (1)

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This example workflow aligns short sequencing reads to a reference genome using Bowtie and generates a SAMtools pileup file. By analysing an actual data set (SNP detection in N. vitripennis) and translating this analysis pipeline into a Taverna workflow, I was able to come up with an easy way of using Taverna for such analysis. I created a Java API (with my limited Java experience) that wraps the command line programs used in the analysis pipeline: Bowtie and some of the SAMtools. Instead of ...

Created: 2010-09-16

Running a picard tool in the #KNIME workfl... (1)

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Running a picard tool in the #KNIME workflow engine . See my blog http://plindenbaum.blogspot.fr/2013/07/running-picard-tool-in-knime-workflow.html

Created: 2013-07-18

Credits: PL

RNA-Seq workflow with TopHat and Cufflinks... (1)

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Created: 2013-11-09 | Last updated: 2014-04-10

Credits: zohim Carol Lushbough Bioextract BioExtract Server for Genomics

Clustered heatmap of signals around the TSSs (1)

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Galaxy workflow based on deepTools which creates a clustered heatmap of signals around the TSS. One bigwig file is needed as input with the signal and an annotation file with your TSS regions. The output will be a heatmap. You can create such a bigwig file with the bamCorrelate toolFor more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.

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

Credits: Björn Grüning

Heatmap of read coverages (1)

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Created: 2014-04-03

Credits: Björn Grüning

Heatmap of read coverages (single BAM file) (1)

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Created: 2014-04-03

Credits: Björn Grüning

Compute and correct GC bias in NGS data (1)

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Galaxy workflow based on deepTools which will compute and correct GC bias in your NGS data. For more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.

Created: 2014-04-03

Credits: Björn Grüning

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 : 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 : 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 : 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

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

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

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

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

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

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 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

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 : 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 : 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 : 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 : 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

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