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Old 03-27-2019, 06:01 AM   #3
NDUFB11
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Location: Italy

Join Date: Jul 2017
Posts: 34
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Hi GenoMax,

unfortunately writing the entire path didn't help,

there must be something in my index structure command line that need to be adjusted I guess.

the problem is that if I want to use the option

Code:
--quantMode TranscriptomeSAM GeneCounts
I need to use the fasta format along with the GTF format for the index, otherwise I can get the genomeParameters.txt by using only the fasta format
Thank you for you answer anyways
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