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. 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 big files (>500mb) it is highly recommended you use the 2nd approach./

Inputting Files

Design

As you can see, you have 3 boxes from which you can choose to input a design (going from left to right) :

1. Either inputing an IUPAC or a design.csv file which is in a mounted folder (meaning you started the tool with the -v parameter and referenced a local folder).

2. Give a url to a location where a design file reside.

3. Upload a local file yourself.

Config

As you can see, you have 3 boxes from which you can choose to input a config (going from left to right) :

1. config.json file which is in a mounted folder (meaning you started the tool with the -v parameter and referenced a local folder).

2. Give a url to a location where a config.json file reside.

3. Upload a local config.json file yourself.

Reads Files (Currently support Fastq)

Choosing matching type

We currently supply 3 method for matching between a read and a variant (You can choose more than 1):

1. BarcodeAligner : Looks for a perfect match between the variant barcode and the location of the barcode in the read. (Remember the config.json gives the exact location of the barcode.)

2. NEditBarcodeAligner : Looks for the variant barcode with the smallest edit distance while allowing only variants with a edit distance smaller than n (A parameter you can set in the config file 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:

pageAnalysis