Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update who sends AWS.md #156

Merged
merged 1 commit into from
Jul 13, 2024
+1 −1
Merged

Update who sends AWS.md #156

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion instructors/faq.md
View file
Original file line number Diff line number Diff line change
@@ -4,8 +4,8 @@

Thank you for your interest in hosting or teaching a Genomics workshop. Below you will find answers to some frequently asked questions about this curriculum. If the answer to your question doesn't appear, please contact [team@carpentries.org](mailto:team@carpentries.org).

- [For Hosts](#hosts)

Check warning on line 7 in instructors/faq.md

GitHub Actions / Build markdown source files if valid 

 [missing anchor]: [For Hosts](#hosts)
- [For Instructors](#instructors)

Check warning on line 8 in instructors/faq.md

GitHub Actions / Build markdown source files if valid 

 [missing anchor]: [For Instructors](#instructors)

## <a id="hosts"></a> Hosts

@@ -62,7 +62,7 @@

### How will my learners get connection and log-in information?

The Carpentries Workshop and Logistics Manager will provide Instructors with connection information for AMI instances the day before the workshop. Enough instances will be provided for each learner, and if requested, for each workshop helper, to have their own individual instance. Instructors can make connection information available to learners through the workshop Etherpad.
The Carpentries Workshops and Instruction Team will provide Instructors with connection information for AMI instances the day before the workshop. Enough instances will be provided for each learner, and if requested, for each workshop helper, to have their own individual instance. Instructors can make connection information available to learners through the workshop Etherpad.

### I want to teach the optional R lesson. Can I do that?

Unchanged files with check annotations Beta

View file
index.md
## Frequently Asked Questions
Read our [FAQ](/genomics-workshop/faq) to learn more about Data Carpentry's Genomics workshop, as an Instructor or a workshop host.

Check warning on line 21 in index.md

GitHub Actions / Build markdown source files if valid 

 [missing file]: [FAQ](/genomics-workshop/faq)
::::::::::::::::::::::::::::::::::::::::::::::::::
View file
learners/setup.md
| Software | Version | Manual | Available for | Description |
| -------- | ------- | ------ | --------------------- | --------------------------------------------------------------------- |
| [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | 0\.11.9 | [Link](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/) | Linux, MacOS, Windows | Quality control tool for high throughput sequence data. |

Check warning on line 149 in learners/setup.md

GitHub Actions / Build markdown source files if valid 

 [uninformative link text]: [Link](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/)
| [Trimmomatic](https://www.usadellab.org/cms/?page=trimmomatic) | 0\.39 | [Link](https://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf) | Linux, MacOS, Windows | A flexible read trimming tool for Illumina NGS data. |

Check warning on line 150 in learners/setup.md

GitHub Actions / Build markdown source files if valid 

 [uninformative link text]: [Link](https://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf)
| [BWA](https://bio-bwa.sourceforge.net/) | 0\.7.17 | [Link](https://bio-bwa.sourceforge.net/bwa.shtml) | Linux, MacOS | Mapping DNA sequences against reference genome. |

Check warning on line 151 in learners/setup.md

GitHub Actions / Build markdown source files if valid 

 [uninformative link text]: [Link](https://bio-bwa.sourceforge.net/bwa.shtml)
| [SAMtools](https://samtools.sourceforge.net/) | 1\.9 | [Link](https://www.htslib.org/doc/samtools.html) | Linux, MacOS | Utilities for manipulating alignments in the SAM format. |

Check warning on line 152 in learners/setup.md

GitHub Actions / Build markdown source files if valid 

 [uninformative link text]: [Link](https://www.htslib.org/doc/samtools.html)
| [BCFtools](https://samtools.github.io/bcftools/) | 1\.9 | [Link](https://samtools.github.io/bcftools/bcftools.html) | Linux, MacOS | Utilities for variant calling and manipulating VCFs and BCFs. |

Check warning on line 153 in learners/setup.md

GitHub Actions / Build markdown source files if valid 

 [uninformative link text]: [Link](https://samtools.github.io/bcftools/bcftools.html)
| [IGV](https://software.broadinstitute.org/software/igv/home) | [Link](https://software.broadinstitute.org/software/igv/download) | [Link](https://software.broadinstitute.org/software/igv/UserGuide) | Linux, MacOS, Windows | Visualization and interactive exploration of large genomics datasets. |

Check warning on line 154 in learners/setup.md

GitHub Actions / Build markdown source files if valid 

 [uninformative link text]: [Link](https://software.broadinstitute.org/software/igv/download)

Check warning on line 154 in learners/setup.md

GitHub Actions / Build markdown source files if valid 

 [uninformative link text]: [Link](https://software.broadinstitute.org/software/igv/UserGuide)
### QuickStart Software Installation Instructions