Difference between revisions of "SRA to FASTQ (workflow)"
m (Protected "SRA to FASTQ (workflow)": Autogenerated page ([edit=sysop] (indefinite))) |
(Automatic synchronization with BioUML) |
||
| Line 5: | Line 5: | ||
== Workflow overview == | == Workflow overview == | ||
[[File:SRA-to-FASTQ-workflow-overview.png|400px]] | [[File:SRA-to-FASTQ-workflow-overview.png|400px]] | ||
| + | == Description == | ||
| + | This workflow can be used to convert SRA data files (e. g. from NGS/RNA-seq experiments) into FASTQ files. The FASTQ format is widely used by a number of tools and the geneXplain platform is among them; on the other hand, NGS data are often collected in SRA format, thus the conversion of SRA format into FASTQ format is an important function. | ||
| + | |||
| + | In this workflow the input fastq files are subjected to the tool FUSION finder | ||
| + | |||
| + | '''http://genexplain-platform.com/bioumlweb/#de=analyses/Galaxy/gene_fusion/fusionfinder''' | ||
| + | |||
| + | |||
| + | |||
| + | The Fusion finder detects fusions and converts the SRA files into FASTQ files which can be used as an input for other workflows. | ||
| + | |||
| + | |||
| + | |||
| + | '''Note. '''Working with NGS data in SRA and FASTQ formats requires substantial work space available in your user account. Feel free to contact us (info@genexplain.com) to upgrade your account with additional disk space. | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
== Parameters == | == Parameters == | ||
;Input folder | ;Input folder | ||
Latest revision as of 16:34, 12 March 2019
- Workflow title
- SRA to FASTQ
- Provider
- geneXplain GmbH
[edit] Workflow overview
[edit] Description
This workflow can be used to convert SRA data files (e. g. from NGS/RNA-seq experiments) into FASTQ files. The FASTQ format is widely used by a number of tools and the geneXplain platform is among them; on the other hand, NGS data are often collected in SRA format, thus the conversion of SRA format into FASTQ format is an important function.
In this workflow the input fastq files are subjected to the tool FUSION finder
http://genexplain-platform.com/bioumlweb/#de=analyses/Galaxy/gene_fusion/fusionfinder
The Fusion finder detects fusions and converts the SRA files into FASTQ files which can be used as an input for other workflows.
Note. Working with NGS data in SRA and FASTQ formats requires substantial work space available in your user account. Feel free to contact us (info@genexplain.com) to upgrade your account with additional disk space.
[edit] Parameters
- Input folder
- Output folder
