STAR problem

Question

[yufgua]

Hi, I am just learning RNA-seq analysis, right now I am using STAR to build a genome index, however my code not working, Can anyone help me to check? with greeting:)

STAR 
--runMode genomeGenerate 
--genomeDir index
--runThreadN 10 
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/GENOME --genomeFastaFiles 
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.dna.chromosome.1.fa
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.dna.chromosome.2.fa
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.dna.chromosome.3.fa
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.dna.chromosome.4.fa
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.dna.chromosome.5.fa
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.dna.chromosome.Mt.fa
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.dna.chromosome.Pt.fa 
--sjdbGTFfile /Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.54.gtf
--sjdbOverhang 99

[ATpoint]

What is the error? Usually one first concatenates all fasta files together and then runs star on that. Please show any error message. You will also need \ at the end of every but the last line if code is indeed in multiple lines.

[rpolicastro]

The -- at the beginning of the fasta file paths is probably breaking it too. In addition to concatenating the fasta files you can also provide them as space separated.