This is a test version of Biostars. For the public version, visit https://www.biostars.org.
STAR indexing doubt

noobie question: just started an indexing of a genome: with the command 

STAR --runMode genomeGenerate --runThreadN 4 --genomeDir STAR_index/ --genomeFastaFiles genome.fa --sjdbGTFfile genome.gff3 --sjdbGTFtagExonParentTranscript Parent --sjdbOverhang 100 --limitGenomeGenerateRAM 16000000000

Its generating a bunch of SA_* files in the STAR_index directory. From the STAR manual i dont really get what these files are, and given that everyone is 1.6G im a bit concerned about this. Could you help me?

index star
• 3,047 views • link
written by Marshall • Marshall

1 answer

Files you are seeing are part of STAR's genome index. From STAR manual:

Genome files comprise binary genome sequence, suffix arrays, text chromosome names/lengths, splice junctions coordinates, and transcripts/genes information. Most of these files use internal STAR format and are not intended to be utilized by the end user. It is strongly not recommended to change any of these file with one exception: you can rename the chromosome names in the chrName.txt keeping the order of the chromosomes in the file: the names from this file will be used in all output files (e.g. SAM/BAM).

• 0 views • link
written by GenoMax GenoMax

Thanks! it doesnt say if all these files correspond to each scaffold/chromosome in the fasta file, what do you think? im just afraid of creating 500 SA files (given that here i have more than 500 scaffolds).

• 0 views • link
written by Marshall • Marshall

Don't worry about the structure of the files. Each program uses its own arrangement. As long as the job completes without any errors, you would be ready to go.

• 0 views • link
written by GenoMax GenoMax

thanks man, while submitting that to the server (thus the star command is running into a .sh script submitted with qsub) i got

/home/me/.bash_profile: line 1: ./.bashrc: No such file or directory

but the process is running anyway. Could you tell me why?

• 0 views • link
written by Marshall • Marshall

What shell are you using? What does echo $SHELL produce?

• 0 views • link
written by GenoMax GenoMax

Looks like you are either missing .bashrc file in your profile or there is a mistake in your .bash_profile where it references that file. Do you get a listing for these files by doing ls -a ~/.bash*?

• 0 views • link
written by GenoMax GenoMax

yep i get .bash_profile and .bashrc files

• 0 views • link
written by Marshall • Marshall

What does head -7 ~/.bash_profile produce?

• 0 views • link
written by GenoMax GenoMax

Do you get an error if you try to run it as is? That line probably needs to be source ~/.bashrc

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this