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Old 02-19-2019, 08:52 AM   #1
NDUFB11
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Location: Italy

Join Date: Jul 2017
Posts: 34
Default STAR read Mapping

Hello everybody,

I kindly need your help again ...

I want to map my reads on the genome using STAR but for some reason I get an error that I don't know how to solve

When I type the command line here is what I get:



Code:
Patrizios-MBP:processing patrizio$ STAR --genomeDir genome/star/ --runThreadN 4 --readFilesIn clipped/SRR359063_1.fastq.zip clipped/ SRR359063_2.fastq.zip --outFileNamePrefix mapping/star/SRR359063. --outSAMattributes All --outSAMtype BAM SortedByCoordinate --readFileCommand gunzip
EXITING: FATAL INPUT ERROR: unrecoginzed parameter name "readFileIn" in input "Command-Line-Initial"
SOLUTION: use correct parameter name (check the manual)

Feb 19 18:49:56 ...... FATAL ERROR, exiting[/B]

I also tried to process unzipped files and remove the command to execute each single input file --readFileCommand, but still I can't go further,

I have a MacOs terminal,


thank you

Patrizio

Last edited by GenoMax; 02-19-2019 at 09:16 AM. Reason: Added [code] tags
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