Trouble to generate genome indexes for human RNA-seq reads in STAR
Entering edit mode
4 weeks 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:

Thank you so much!

STAR RNA-Seq • 195 views
Entering edit mode

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


Login before adding your answer.

Traffic: 1689 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6