Matching and Analysis

If you want to preform both variant-read matching and analysis.

Starting the tool

There are 2 basic ways you can start the tool with. A simple one, which means you will upload all the input files manually:

$ docker run -p 5000:5000 solqc/tool

Or with an additional parameter (-v), which will allow you to access local files directly on the app by:

$ docker run -p 5000:5000 -v path/to/folder_with_data:/solqc/data solqc/tool

If you want to analyse large files (>500mb) it is highly recommended you use the 2nd approach.

Inputting Files

Design

As you can see, you have 2 boxes from which you can choose to input a design (going from left to right) :

1. Upload a local design.csv file yourself.

2. Inputing an IUPAC String.

NGS Files (Currently supports Fastq)

Here you have 3 options:

1. Uploading a zip containing all your fastq files (using Upload File).

2. Uploading a single fastq file (using Upload File).

3. Selecting your files from exisiting files if you mounted files using the -v option as described in Starting the tool .

Library Configuration

Add library configurations as described in the preparation section.

Choosing matching type

We currently supply 3 methods for matching between a read and a variant:

1. BarcodeAligner : Looks for a perfect match between the variant barcode and the location of the barcode in the read (as set in the Library Configuration).

2. NEditBarcodeAligner : Looks for the variant barcode with the smallest edit distance while allowing only variants with an edit distance smaller than n (a parameter you can set in the Library Configuration under Barcode Tolerance).

3. EditDistanceAligner : Compute the edit distance between a read and all the variants. Chooses the variant with the smallest edit distance from the read.

Analysis options

You can choose between multiply analysis types which will be added to the report. To get a full depth understanding of our analysis list go to:

Analysis