overcooked-ebiomedpku

Example¶

Step-by-step commands¶

1. Detect TE-derived RNAs¶

TERA detect \
  -fq1 ${fastq1} \
  -fq2 ${fastq2} \
  --TE_bed ${ref_TE_bed} \
  --TE_gtf ${ref_TE_gtf} \
  -p ${prefix} \
  -r ${ref_genome_fasta} \
  -a ${ref_genome_gtf} \
  -t ${nthread}

2. Annotate TE-derived RNAs¶

TERA anno \
  -i ${TERA_detect_gtf} \
  --TE_exon ${TERA_detect_bed} \
  --TE_bed ${ref_TE_bed} \
  -p ${prefix} \
  -a ${ref_genome_gtf}

3. Quantify (exon level)¶

TERA quant \
  -fq1 ${fastq1} \
  -fq2 ${fastq2} \
  -l 1 \
  -q rsem \
  --TE_gtf ${TERA_detect_gtf} \
  --TE_exon ${TERA_anno_bed} \
  -p ${prefix} \
  -r ${ref_genome_fasta} \
  -a ${ref_genome_gtf} \
  -t ${nthread}

4. Quantify (unit and family levels)¶

TERA quant \
  -fq1 ${fastq1} \
  -fq2 ${fastq2} \
  -l 2 \
  --TE_gtf ${ref_TE_gtf} \
  -p ${prefix} \
  -r ${ref_genome_fasta} \
  -a ${ref_genome_gtf} \
  -t ${nthread}