SEXCMD : Created Sex Marker and Determination

USAGE : perl determine.pl sex_marker_filtered.hg38.final.fasta input.fastq.gz 2> /dev/null 1> input.SEX_OUTPUT

SEXCMD is available at https://github.com/lovemun/SEXCMD

The code is written in Perl and bash script. This tool is supported on Linux and needs Python, lastz, blastall and bwa. The tool uses gzip compressed fastq file as input and R1 and R2 file can be used in case of paired-end or mate pair. And you should give marker fasta file path, input fastq file path as auguements.

Required software

1. Python (https://www.python.org/ftp/python/2.7.13/python-2.7.13.msi)
2. bwa(version 7.0 or later) (https://sourceforge.net/projects/bio-bwa/files/)
3. blastall (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
4. lastz(Release 1.02.00) (http://www.bx.psu.edu/~rsharris/lastz/lastz-1.04.00.tar.gz)
5. samtools (https://sourceforge.net/projects/samtools/files/samtools/)
6. R (https://www.r-project.org/)

Input Files

1. Reference genome fasta file (ex. hg38.fa)
2. Input sequence file (ex. ERR000000.fastq.gz)

Example

If you want to create marker file, you can make own sex marker file for your datafiles. There are 6 process steps for creating own sex marker file.

1. Extract sex chromosome from Reference genome(ex. Human)

   python 1.extract_chr_from_REF.py hg38.fasta X

   python 1.extract_chr_from_REF.py hg38.fasta Y

2. Mapping between sex chromosomes

   lastz hg38.chrX.fasta hg38.chrY.fasta --format=maf > chrX_chrY.maf

3. Generate sex marker text file

   python 2.sex_marker.py chrX_chrY.maf hg38.ucsc.gtf 35 > sex_marker.hg38.txt (distance between marker : 35(recommended))

   python 3.sex_marker_filtered.py sex_marker.hg38.txt hg38.ucsc.gtf 151 5 > sex_marker_filtered.hg38.txt (read length : 151 admit missmatch count : 5)

4. Convert sex marker file format(text -> fasta)

   python 4.make_markerFASTA.py sex_marker_filtered.hg38.txt

5. Filtered ONLY MAPPED to chrX, chrY

   blastn -db hg38.fa -query sex_marker_filtered.hg38.fasta -num_threads 4 -word_size 8 -outfmt 7 > sex_marker_filtered.hg38.fasta.blastm9

   python 5.blast_filter.py sex_marker_filtered.hg38.fasta sex_marker_filtered.hg38.fasta.blastm9 sex_marker_filtered.hg38.final.fasta

6. Index sex marker file

   bwa index -a is sex_marker_filtered.hg38.final.fasta

Final sex marker : sex_marker_filtered.hg38.final.fasta

Sex determination

Rscript SEXCMD.R sex_marker_filtered.hg38.final.fasta [1/2/3] [XY/ZW] input.fastq.gz

[1/2/3] : sequencing type (1: Exome sequencing, 2: RNA sequencing, 3: Whole genome sequencing)

[XY/ZW] : Sex determination system

Contact

lovemun@kribb.re.kr

Citation