STAR indexing doubt

Question

[Marshall]

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?

Answer 1

[GenoMax]

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).

[Marshall]

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).

[GenoMax]

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.

[Marshall]

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?

[GenoMax]

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

[Marshall]

it produces /bin/bash

[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*?

[Marshall]

yep i get .bash_profile and .bashrc files

[GenoMax]

What does head -7 ~/.bash_profile produce?

[Marshall]

source ./.bashrc

[GenoMax]

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