erv_genome.pl -stage 1 -stage2 6 -fastq /${i}.fastq.gz
Usage:
erv_se_genome_v2.pl [options]
Options:
-h, -? --help brief help message
-t, --test print out commands without run
--btrim path to btrim (http://graphics.med.yale.edu/trim/)
--tophat path to tophat
--bwa path to bwa
--samtools path to samtools
--filter path to filter (parse_bam.pl)
--bedtools path to bedtools
--genome path to bwa human genome index
--genome_Bowtie2 path to Bowtie2 human genome index
--bed path to bed file of ERVs
--genomefile path to genome size file
--gtf path to gtf file of human gene annotation
--transcriptome path to known transcriptome, used by tophat2
--adaptor path to adaptor files, used by btrim (http://graphics.med.yale.edu/trim/)
--fastq fastq file
--stage start stage (see below)
--stage2 end stage (see below)
Stages:
1 trim adaptors and low quality regions
2 map reads using bwa
3 sort bam file
4 count reads mapped to ERVs
5 map reads using tophat2
6 counts reads mapped to genes