This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Indexing the reference genome
nohup STAR \
  --runMode genomeGenerate \
  --genomeDir /Users/yasi/mockexp/genome/genome_index/ \
  --genomeFastaFiles /Users/yasi/mockexp/genome/GCF_000001405.39_GRCh38.p13_genomic.fna \
  --sjdbGTFfile /Users/yasi/mockexp/genome/genomic.gtf --sjdbOverhang 80 > star_genome_generate.log 2>&1

What I am missing or doing wrong while trying to index the reference genome with STAR?

star
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updated by Ram Ram • written by Yasemin • Yasemin

What I am missing or doing wrong while trying to index the reference genome with STAR?

You need to tell us more. The command looks OK. Is the command not working? Are you getting errors?

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written by GenoMax GenoMax

You didn't tell us the error message or the contents of the log file. Tough to help you without proper information.

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written by Mensur Dlakic Mensur Dlakic

Note: Don't use nohup, it interferes with writing to STDOUT/STDERR. Use a proper utility like screen or tmux instead to run a process that you want to protect from interruption. See: https://unix.stackexchange.com/a/192973/135331

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written by Ram Ram

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