Trouble to generate genome indexes for human RNA-seq reads in STAR
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9 months ago
Júlia • 0

Hi everyone, I´m a masters student and new at bioinformatics. My research is in RNA-Seq analysis, and right now I´m having trouble to generate the genome indexes prior to the alignment in STAR. A couple minutes after lauching the command line, an error message apears that the analysis was aborted by the user, a while after the message "sorting Suffix Array chunks and saving them to disk". I´m trying to execute the command on a linux environment, through WinSCP. Apparently the parameters are correct, including the number of threads used. I don´t know where the problem might be. Any guesses?

This is the command:

/opt/STAR-2.7.9a/bin/Linux_x86_64/STAR --runThreadN 20 --runMode genomeGenerate --genomeDir /home/julia.nicoliello/genome_index --genomeFastaFiles /home/julia.nicoliello/genoma-fasta/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /home/julia.nicoliello/GRCh38.101/Homo_sapiens.GRCh38.101.chr.gtf 

And these are the links to the files I´ve dowmloaded:

http://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/ http://ftp.ensembl.org/pub/release-101/gtf/homo_sapiens/

Thank you so much!

STAR RNA-Seq • 425 views
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How much memory do you have available? Generating STAR indexes requires at least 30-40G of free RAM (if not more).

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Hi! The problem actually was in the number of threads, after setting the runThreadsN parameter to 16 it was possible to complete de command. Thank you!

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