Git Product home page Git Product logo

erasmusmc_assignment's Introduction

Extracting PCR target sequences using primers

The repository has two main scripts that are dedicated to each assignment:

  1. "retrieve_target_sequences.py" for extracting target sequences from the reference genome using the provided list of primers.
  2. "generate_short_hand_annotation.py" for converting the extracted target sequences into short-hand annotations using the provided motif list.

The Data folder contains the provided list of primers and motifs, and the Output folder contains:

  1. "all_amplicons.csv" - the list of all found amplicons along with their location, primers, and sequence;
  2. "target_sequences.fasta" - the fasta format of all extracted target sequences;
  3. "short_hand_annotations.csv" - the short-hand annotations of each target sequence; and
  4. "found_seqs.pickle" - pickle file of all possible amplicons identified.

NOTE: The reference genome used in this project is GRCh38.p13, which can be found #Here

erasmusmc_assignment's People

Contributors

denizy7 avatar

Watchers

 avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.