#  --dta                              reports alignments tailored for transcript assemblers
#  --dta-cufflinks                    reports alignments tailored specifically for cufflinks

#/home/common/hisat2-2.1.0/hisat2 --max-intronlen 10000 -X 1000 -5 10 -3 100 -x /home/common/hisat2-2.1.0/indexes/hs2mmCCMP2099v1 \
#-1 IGHS_RNAseq_2099A_CGATGT_Micromonas_I677_L1_R1.fastq.bz2 \
# -2 IGHS_RNAseq_2099A_CGATGT_Micromonas_I677_L1_R2.fastq.bz2 \



/home/common/hisat2-2.1.0/hisat2 --max-intronlen 10000  -x /home/common/hisat2-2.1.0/indexes/sc3/genome \
-1 ../Cleveland/trim001A_S50_R1.fastq \
-2 ../Cleveland/mjo_001A_S50_L005_R2_001.fastq \
--dta --dta-cufflinks --novel-splicesite-outfile novel1A_50.bed --fr -S hs1A_50.sam  --un hs2unmapped1A_50 --un-conc hs2unconc1A_50

/home/common/hisat2-2.1.0/hisat2 --max-intronlen 10000  -x /home/common/hisat2-2.1.0/indexes/sc3/genome \
-1 ../Cleveland/trim001B_S51_R1.fastq \
-2 ../Cleveland/mjo_001B_S51_L005_R2_001.fastq \
--dta --dta-cufflinks --novel-splicesite-outfile novel1B_51.bed --fr -S hs1B_51.sam  --un hs2unmapped1B_51 --un-conc hs2unconc1B_51

/home/common/hisat2-2.1.0/hisat2 --max-intronlen 10000  -x /home/common/hisat2-2.1.0/indexes/sc3/genome \
-1 ../Cleveland/trim001C_S52_R1.fastq \
-2 ../Cleveland/mjo_001C_S52_L005_R2_001.fastq \
--dta --dta-cufflinks --novel-splicesite-outfile novel1C_52.bed --fr -S hs1C_52.sam  --un hs2unmapped1C_52 --un-conc hs2unconc1C_52

/home/common/hisat2-2.1.0/hisat2 --max-intronlen 10000  -x /home/common/hisat2-2.1.0/indexes/sc3/genome \
-1 ../Cleveland/trim001D_S53_R1.fastq \
-2 ../Cleveland/mjo_001D_S53_L005_R2_001.fastq \
--dta --dta-cufflinks --novel-splicesite-outfile novel1D_53.bed --fr -S hs1D_53.sam  --un hs2unmapped1D_53 --un-conc hs2unconc1D_53