n=1
wdir=/nfs/srv/databases/ngs/russal2010/pr12
trim='java -jar /nfs/srv/databases/ngs/suvorova/trimmomatic/trimmomatic-0.30.jar'
idx=/nfs/srv/databases/ngs/russal2010/pr11/index/chr19.idx
before=${wdir}/reads/chr19.${n}.fastq
after=${wdir}/reads/chr19.${n}.trim.fastq
gtf=/nfs/srv/databases/ngs/Human/rnaseq_reads/gencode.v19.chr_patch_hapl_scaff.annotation.gtf
samfile=${wdir}/map/chr19.${n}.sam
bamfile=${wdir}/map/chr19.${n}.bam
sortedbam=${wdir}/map/chr19.${n}.sort.bam
flag_out=${wdir}/map/flgst.${n}.o
samout=${wdir}/map/count.${n}.sam