Dear All,

I have the intention to use STAR for the mapping of my Iontorrent RNA-Seq data. I am new to RNA_seq data analysis and I am confused regarding the way the log.out file content in STAR.

Primarily I am trying to generate the mouse genome indexes using appropriate data downloaded from Ensambl (GRCm38.90) I am using the single-fasta-file (not individual chromosome sets) to build the genome index (2.8GB un-tarred size). I have the matching gtf annotation file in the same directory as well.

My command-line is as follows (12 core CPU & 32 GB RAM):

STAR --runThreadN 20 --runMode genomeGenerate --genomeDir ~/Documents/Mus_Musculus_Genome --genomeFastaFiles Mus_musculus.GRCm38.dna.chromosome.1.fa --sjdbGTFfile Mus_musculus.GRCm38.90.gtf --sjdbOverhang 100

STAR seem to generate a genome index successfully and the terminal window remarks the following:

Nov 22 19:34:11 ..... started STAR run Nov 22 19:34:11 ... starting to generate Genome files Nov 22 19:34:50 ... starting to sort Suffix Array. This may take a long time... Nov 22 19:34:59 ... sorting Suffix Array chunks and saving them to disk... Nov 22 19:49:30 ... loading chunks from disk, packing SA... Nov 22 19:51:30 ... finished generating suffix array Nov 22 19:51:30 ... generating Suffix Array index Nov 22 19:54:23 ... completed Suffix Array index Nov 22 19:54:23 ..... processing annotations GTF Nov 22 19:54:30 ..... inserting junctions into the genome indices Nov 22 19:56:53 ... writing Genome to disk ... Nov 22 19:57:03 ... writing Suffix Array to disk ... Nov 22 19:58:00 ... writing SAindex to disk Nov 22 19:58:04 ..... finished successfully

However, the Log.out file depicts the following which was confusing for me:

Finished loading and checking parameters Nov 22 19:34:11 ... starting to generate Genome files Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 0 "1" chrStart: 0 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 1 "10" chrStart: 195559424 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 2 "11" chrStart: 326369280 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 3 "12" chrStart: 448528384 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 4 "13" chrStart: 568852480 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 5 "14" chrStart: 689438720 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 6 "15" chrStart: 814481408 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 7 "16" chrStart: 918552576 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 8 "17" chrStart: 1016856576 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 9 "18" chrStart: 1112014848 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 10 "19" chrStart: 1202978816 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 11 "2" chrStart: 1264582656 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 12 "3" chrStart: 1446772736 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 13 "4" chrStart: 1606942720 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 14 "5" chrStart: 1763704832 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 15 "6" chrStart: 1915748352 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 16 "7" chrStart: 2065694720 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 17 "8" chrStart: 2211184640 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 18 "9" chrStart: 2340683776 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 19 "MT" chrStart: 2465464320 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 20 "X" chrStart: 2465726464 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 21 "Y" chrStart: 2636906496 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 22 "JH584299.1" chrStart: 2728656896 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 23 "GL456233.1" chrStart: 2729705472 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 24 "JH584301.1" chrStart: 2730229760 ................... Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 60 "GL456382.1" chrStart: 2739666944 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 61 "GL456359.1" chrStart: 2739929088 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 62 "GL456396.1" chrStart: 2740191232 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 63 "GL456368.1" chrStart: 2740453376 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 64 "JH584292.1" chrStart: 2740715520 Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 65 "JH584295.1" chrStart: 2740977664 Number of SA indices: 5305567000

I wonder if those awkward "chr#" chromosome numbers are erroneous

I will be grateful if you may also guide me weather if using a single fasta genome file is fine or not. I am not using the TOPLEVEL files as I have read in several discussions that it might not be the best choice.

Best,

Chet