hisat2+stringtie+ballgown

hisat2 -p 8 --dta -x chrX_data/indexes/chrX_tran -1 chrX_data/samples/ERR188044_chrX_1.fastq.gz -2 chrX_data/samples/ERR188044_chrX_2.fastq.gz -S ERR188044_chrX.sam

samtools sort -o XX.bam xx.sam

stringtie -p 8 -G chrX_data/genes/chrX.gtf -o ERR188044_chrX.gtf–l ERR188044 ERR188044_chrX.bam

stringtie --merge -p 8 -G chrX_data/genes/chrX.gtf -o stringtie_merged.gtfchrX_data/mergelist.txt

stringtie –e –B -p 8 -G stringtie_merged.gtf-o ballgown/ERR188044/ERR188044_chrX.gtf ERR188044_chrX.bam