I ran STAR, but essential output files did not generate.

Question

[ZZOYEA]

Hi all,

I am currently doing RNA-seq analysis, but encountered an issue during the 'genomeGenerate' step with STAR. Can you provide advice on what might be the problem?

My script was:

/home/Tools/STAR-2.6.1e/bin/Linux_x86_64/STAR --runMode genomeGenerate --runThreadN 1 --genomeDir forRsem_cuffmerge --genomeFastaFiles /media/Index/homo_sapiens/hg19/Sequence/WholeGenomeFasta/genome.fa --outFileNamePrefix forRsem_cuffmerge/hg19 --sjdbGTFfile /media/RNA-seq/07_cuffmerge/merged_asm/results/merged_strand.gtf --sjdbOverhang 100

Although there were no specific error messages, and the 'finished successfully' message appeared, some essential files required for running RSEM did not get generated.

The files I got(16 files):

chrName.txt/
chrNameLength.txt/
chrStart.txt/
exonGeTrInfor.tab/
exonInfo.tab/
geneInfo.tab/
Genome/
genomeParameters.txt/
hg19Log.out/
SA/
SAidnex/
sjdbInfo.txt/
sjdbList.fromGTF.out.tab/
sjdbList.out.tab/
transcriptInfro.tab/

There is no 'hg19.seq', 'hg19.transcripts.fa', 'hg19.n2g.idx.fa', 'hg19.idx.fa', 'hg10.ti', 'hg19.grp', 'hg19.chrlist' files

Can someone help me? Why aren't all of those important files created?

[ATpoint]

STAR output is what you see. Which manual do you refer to when you say that STAR is supposed to output all these other files?

Answer 1

[ZZOYEA]

Thank you! I found out that all those files come out if I use rsem-prepare-reference, not STAR.