Skip to content

README.md

Latest commit

 

History

History
33 lines (25 loc) · 1.28 KB

README.md

File metadata and controls

33 lines (25 loc) · 1.28 KB
Raw

Call Hops for Inducible Calling Cards Paper

This document was written by Rebecca Chase. Code written and executed by Allen Yen and Simona Sarafinovska

This code takes fastq files generated from a Bulk Calling Cards experiment and prepares the reads for alignment. After alignment, the reads are tagged with barcodes to get a list of reads with transposon insertions.

Installing / Getting started

This code relies on the following tools and packages: python3 cutadapt version 2.9 umi-tools version 1.0.0 bowtie2 version 2.4.2 bwa version 0.7.17 samtools version 1.13 HOMER (http://homer.ucsd.edu/homer/download.html)

Features

Code consists of an sbatch file where the following variables must be assigned:

  • GENOME
  • PROJECT_DIR
  • BOWTIE2_INDEX_PATH_AND_PREFIX
  • TWO_BIT_PATH
  • A manifest file that allows information to be pulled into the sbatch script.
  • A SRT Barcode text file where one can input SRT barcodes used
  • .py files used to filter files, tag reads, and create/sort bam files

HOMER was run using findMotifsGenome.pl with the output BED file, the mm10 genome, and a size of 200.

Additional Information

This code was eventually worked into the project nf-core/callingcards: https://github.com/nf-core/callingcards See the associated paper here: https://doi.org/10.1002/cpz1.883