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Forum: Bioinformatics 12-18-2018, 06:49 AM
Replies: 1
Views: 900
Posted By staszekdh
Problem solved. I used HISAT2 with...

Problem solved. I used HISAT2 with "--rna-strandness RF" + stringtie and now I get reasonable results.

HISAT2:



$HISAT2_HOME/hisat2 -q \
-p 10 \
-x...
Forum: Bioinformatics 12-12-2018, 01:29 PM
Replies: 1
Views: 900
Posted By staszekdh
cufflinks does not understand strands?

Dear All,

I used STAR to map paired-end reads onto the reference genome:


~/apps/STAR/bin/Linux_x86_64/STAR --runMode alignReads \
--runThreadN 10 \
--genomeDir...
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