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Old 12-18-2018, 06:49 AM   #2
staszekdh
Junior Member
 
Location: Poland

Join Date: Dec 2018
Posts: 2
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Problem solved. I used HISAT2 with "--rna-strandness RF" + stringtie and now I get reasonable results.

HISAT2:

Code:
$HISAT2_HOME/hisat2 -q \
                -p 10 \
                -x ../../../genome/genome/XX \
                -1 ../B1R_S1_R1_001.clean.fastq \
                -2 ../B1R_S1_R2_001.clean.fastq \
                -S out_mock_rep1_clean/alns.sam \
                --fr \
                --rna-strandness RF \
                --dta
stringtie:

Code:
~/apps/stringtie-1.3.5.Linux_x86_64/stringtie \
	../hisat/out_mock_rep1_clean/alns.sorted.bam \
	-o ./out_mock_rep1_clean/out.gtf \
	-p 10 \
	--fr \
        -G ../../../genome/xxx.gff
BTW: I found this post useful
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