QuantTE is an analsis pipeline that utilize the RNA-Seq data and RepeatMasker table to quantify the repeat element. There are two main stages for QuantTE: extraction and quantification. The first stage used the RepeatMasker table and genome sequences to extract the transposable element in interest while the second stage used Kallisto to quantify the abundance of transposable element.
- Extract stage:
python3 QuantTE/main.py --extract --input input.json
- Quant stage:
python3 QuantTE/main.py --kallisto --input input.json
- Run Complete Analysis
python3 QuantTE/main.py --extract --kallisto --input input.json
- Complete analysis (Single-End Reads)
{
"output_dir": "path of output directory",
"genome_fasta": "path of genomic sequence",
"transcript_fasta": "path of transcriptomic sequence",
"repeat_masker_dir": "directory of repeat masker tables",
"read_label": ["condition.1", "condition.2"],
"read_fastq": ["condition.1.fastq", "condition.2.fastq"],
"TE_fasta": "(output) path of transposon element sequence"
}
- Complete analysis (Paired-End Reads)
{
"output_dir": "path of output directory",
"genome_fasta": "path of genomic sequence",
"transcript_fasta": "path of transcriptomic sequence",
"repeat_masker_dir": "directory of repeat masker tables",
"read_label": ["condition.1", "condition.2"],
"read_fastq": ["condition.1.R1.fastq condition.1.R2.fastq", "condition.2.R1.fastq condition.2.R2.fastq"],
"TE_fasta": "(output) path of transposon element sequence"
}