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NGS

This repository contains multiple Python scrips to work on NGS dataset.

1) NCBI to UCSC SAM

The script, ncbi_to_ucsc.py, takes an input file with NCBI chromosome codes and one or more SAM/BAM files with NCBI chromosome identifiers, and outputs modified SAM/BAM files with UCSC chromosome identifiers. Run the script using the following command: python2 ncbi_to_ucsc.py NC_chr.txt input.sam output.sam

Requirements

  • Python 2.7

  • NC_chr.txt mapping file

  • NC_chr.txt: Path to the mapping file downloaded from the NCBI website.

  • input.sam: Path to the input SAM file.

  • output.sam: Path to the output SAM file in UCSC format.

Output

The output file will have the same format as the input file but with UCSC chromosome names instead of NCBI chromosome names.

NC_chr.txt

The mapping file NC_chr.txt can be downloaded from the NCBI website using the following URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_assembly_report.txt