Usage

General Use

Generating Plots

transposcope align <index_type> <index> <bam> <me_reference> <host_reference> <sample_id>

Input	Discription
index_type	The program used to identify the insertion sites { tipseqhunter or melt }
index	Index table
bam	Bam file containing reads
me_reference	The reference sequence of the mobile element being evaluated
host_reference	A folder containing the reference sequences for the host genome chromosomes E.G. HG38/
sample_id	Unique identifier for the output to avoid overwriting previous output

Optional Flags

• --genes <path/to/refFlat.txt>
  • This flag will add the nearest gene to the insertion table within the visualization. Use the refFlat.txt file that matches the reference genome.
• --group1 <group_name>
  • Outer level group name used for grouping samples together
• --group2 <group_name>
  • Inner level group name used for grouping samples together.
  • An example would be the outer level group being the sample id and the inner level group being the sample type (Normal, Met, etc.)
• --keep_files
  • This flag will keep the intermediate files created in a directory called 'output'. There are additional optional parameters that can be viewed by passing the help flag.

transposcope align --help

Viewing Plots

transposcope view path/to/alignment/output/web

Publishing Plots to GitHub

1. Create a new repository on GitHub. https://help.github.com/en/articles/creating-a-new-repository

2. Initialize git in the web folder output from the aligning step.

cd <path/to/alignment/output/web>
git init
git add .
git commit -m 'committing generated plots'

3. Link the Github repository created in step 1 to your local git folder

git remote add origin <<https://github.com/user/repo.git>>

4. Push the local folder to Github

git push origin master

5. Set up GitHub pages to view the output https://help.github.com/en/articles/configuring-a-publishing-source-for-github-pages#enabling-github-pages-to-publish-your-site-from-master-or-gh-pages