Example pipeline¶

Use the upstream example script:

https://github.com/janky-yz/SERVE/blob/main/script/example.sh

Step-by-step commands¶

1. Detecting expressed ERVs per sample¶

SERVE.py --fastq1 ${fastq1} --fastq2 ${fastq2} \
	-e ${ref_erv} -r ${ref_genome} -a ${ref_annotation} \
	-t ${nthread} -p ${prefix}

2. Merging ERV transcripts from multiple samples¶

nsample=$(ls ${wrk_dir}/3_qc/*gtf | wc -l)
ls ${wrk_dir}/3_qc/*gtf > ${wrk_dir}/gtf.list
SERVE_merge.py -i ${wrk_dir}/gtf.list -n ${nsample} \
	-r ${ref_genome} -t ${nthread}

3. Quantifying ERVs¶

ERV_annotation=${wrk_dir}/SERVE_ERV_merge.gtf
merge_annotation=${wrk_dir}/GRCh38_ERV_merge.gtf

cat ${ref_annotation} ${ERV_annotation} > ${merge_annotation}
SERVE_quant.py --fastq1 ${fastq1} --fastq2 ${fastq2} \
	-r ${ref_genome} -a ${merge_annotation} -t ${nthread} -p ${prefix}

4. Merging quantification results and QC¶

ls ${wrk_dir}/*genes.results > ${wrk_dir}/sample.list
SERVE_quant_QC.py -i ${wrk_dir}/sample.list -p ${prefix}