This program reads a set of FASTQ files from a paired-end ddRAD sequencing Aedes albopictus sample (nlaIII and mluCI restriction enzymes) and predicts the sex of the sample. Prediction works best for libraries prepared with fragment size selection of ~300 bp.
Make sure that the following are accessable in your $PATH:
- samtools
- bedtools
- bowtie2
The following R libraries are also required:
- optparse
- e1071
- ps
Clone the github repository:
git clone https://github.com/pearg/albo_spm.git
[Optional] Add the directory to your $PATH environment variable:
export PATH=/path/to/cloned/repo/albo_spm:$PATH
Usage information can be displayed using the -h or --help argument:
$ ./albo_spm.R -h
Usage: ./albo_spm.R [OPTIONS] --r1 [R1_FASTQ] --r2 [R2_FASTQ] --output [OUTPUT_FILENAME]
Predict sex of Aedes albopictus from ddRAD sequencing (nlaIII and mluCI restriction enzymes).
Options:
--r1=R1_FASTQ
R1 FASTQ file [REQUIRED]
--r2=R2_FASTQ
R2 FASTQ file [REQUIRED]
--output=OUTPUT_FILENAME
Output filename [REQUIRED]
--sample_name=SAMPLE_NAME
Sample name
--detailed_output
Output detailed results including estimated frgment size and control depth of coverage
--save_rdata_file=RDATA_FILENAME
RData filename to save objects for debugging
--keep_tmp_files
Keep tmp files for debugging
--threads=N
Number of threads to use [default: 2]
--version
Print version and exit
-h, --help
Show this help message and exit
Example:
albo_spm.R \
--r1 sample_01.R1.fq \
--r2 sample_01.R2.fq \
--output sample_01.sex.tsv \
--sample_name sample_01 \
--threads 8
Example output:
$ cat sample_01.sex.tsv
sample class probability prob_female prob_male
sample_01 Female 0.9648 0.9648 0.0352