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Added the line of command for our usage statement #10

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Added the line of command for our usage statement #10

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bf2e761
Added the line of command
ccialek Jan 27, 2019
92ce6cc
Added info for seqfileconverter users
ccialek Jan 27, 2019
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8 changes: 5 additions & 3 deletions README.md
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Expand Up @@ -11,6 +11,8 @@ and using Python to solve problems or automate tasks.

## Getting Started

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you should be able to add the image file now, but will you make a new folder called "images" and move it there. Then add it in using markdown described here https://guides.github.com/features/mastering-markdown/

Sequencing File Conveter allows the user to swap the format of their nucleic acid sequencing file (allowed file types: .qseq, .fastq, or .sam). Please refer to the seqfileconverter usage diagram to view the current supported swaps.

### Prerequisites

Utility scripts are written in Python3.
Expand All @@ -29,17 +31,17 @@ Tests have not yet been created for this repository.

### Usage

To run file converter:
To run sequencing file converter:
```
python <command here>
python seqfileconverter -f <input file> -o <output file> -d <discard file> -m <metadata file> -t <file type>
```
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Can you add the line python seqfileconverter -h and also the output of that? And is it seqfileconverter or seqfileconverter.py?


## Contributing

This is a beginner, educational repository for students learning Python or R to contribute to. We are a small group of students at CSU studying biology and learning code through hands-on activities, please contact a member through the webpage to ask about joining before you contribute to this repository.

### Proposed ideas:
* qSeq-FastQ converter
* qSeq to/from SAM file converter (can be added as a module to seqfileconverter)
* demultiplex libraries

## Authors
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