Workflows

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Showing 23 results. Use the filters on the left and the search box below to refine the results.
Type: Galaxy Licence: by-sa

Workflow VCaP RNA-Seq Fusion gene detection with ST... (1)

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The end-to-end workflow starts by obtaining paired-end RNA-Seq data of the VCaP cell line via EGA. Galaxy determines the file type automatically with its built-in format detection system. The reads will be clipped before an alignment with STAR and STAR produces several output files that can be used for different analysis. The last tool is STAR-Fusion which was able to confirm the TMPRSS2-ERG fusion gene. 

Created: 2016-08-31 | Last updated: 2016-08-31

Credits: User Y. Hoogstrate

Workflow vir-representative (1)

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Retrieve from NCBI and reduce redundancy in the viral database.

Created: 2016-08-09 | Last updated: 2016-08-09

Credits: User Juliana Pegoraro

Workflow Galaxy workflow for the identification of ... (1)

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This approach screens three proteins against a given genome sequence, leading to a genome position were all three genes are located nearby. As usual in Galaxy workflows every parameter, including the proximity distance, can be changed and additional steps can be easily added. For example additional filtering to refine the initial BLAST hits, or inclusion of a third query sequence.https://github.com/bgruening/galaxytools/tree/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby

Created: 2015-03-17

Credits: User Björn Grüning

Workflow Galaxy workflow for the identification of ... (1)

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This approach screens two proteins against all nucleotide sequence from the NCBI nt database within hours on our cluster, leading to all organisms with an inter- esting gene structure for further investigation. As usual in Galaxy workflows every parameter, including the proximity distance, can be changed and additional steps can be easily added. For example additional filtering to refine the initial BLAST hits, or inclusion of a third query sequence.https://github.com/bgruening/galaxytools/tr...

Created: 2015-01-25

Credits: User Björn Grüning

Uploader

Workflow pipeline5 (1)

https://drive.google.com/a/ganitlabs.in/file/d/0B4KdY3xOOGLvY0twenNJWlVRTU0/edit?usp=sharing

Created: 2015-01-09 | Last updated: 2015-01-09

Credits: User Chetan Joshi

Workflow 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: User Björn Grüning

Workflow Remove "chr" from the beginning of genomic... (1)

This Galaxy workflow will remove the 'chr' string from the beginning of every line in genomic interval files.

Created: 2014-04-03

Credits: User Björn Grüning

Workflow Add "chr" to the first column of a 6 colum... (1)

That workflow is changing the chromosome naming in your BED file. It will add the string 'chr' at the beginning of every line.

Created: 2014-04-03

Credits: User Björn Grüning

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

Galaxy workflow based on deepTools which creates a clustered heatmap of the read coverage. One BAM file will be used as input and a heatmap will be the output.For more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.

Created: 2014-04-03

Credits: User Björn Grüning

Workflow Heatmap of read coverages (1)

Galaxy workflow based on deepTools which creates a clustered heatmap of the read coverage. Two BAM files will be used as input and a heatmap will be the output.For more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.

Created: 2014-04-03

Credits: User Björn Grüning

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