I am very new to RNA-Seq. I am trying to align my samples with STAR. I am generating the genome index myself. Because I was hoping to add the spike-in sequence to the GTF and FASTA files. 

I am downloading the GTF file from here: ftp://ftp.ensembl.org/pub/release-86/gtf/mus_musculus/

There are 2 GTF files one with CHR in the name and one without. I was wondering which one should I use and how they are different. I have not figured this out just by opening the files. 

Thank you,

If you are not sure too, would you please let me know which one you use for your analysis. 

The one with CHR seems to have more lines and it seems to be scaffold genes. Am I missing something? 
The one without 'chr' contains annotations for genes on unplaced or unlocalized contigs, while the one with 'chr' only contains annotation for assembled chromosomes, both of them have no prefix 'chr' in chromosome name, see this example:

    zcat Danio_rerio.GRCz10.87.gtf.gz | cut -f1 | awk '{dict[$1]++}END{for(i in dict) print i, dict[i]}' 
    KN150307.1 9
    KN150451.1 7
    KN150002.1 3
    KN149765.1 3
    KN149909.1 15
    KN149998.1 13
    #!genebuild-last-updated 1
    KN150027.1 10
    KN149917.1 7
    KN150188.1 24
    ...
    13 43069
    20 48282
    KN150399.1 11
    KN150221.1 10
    KN150670.1 32
    KN149696.1 225
    21 40566
    ...

    
    zcat Danio_rerio.GRCz10.87.chr.gtf.gz | cut -f1 | awk '{dict[$1]++}END{for(i in dict) print i, dict[i]}' | head
    #!genebuild-last-updated 1
    MT 147
    #!genome-date 1
    10 40589
    11 40971
    12 39371
    13 43069
    20 48282
    21 40566
    14 35910