# STAR Indexing Diference for Small and Large Genome File Output

I have a quick doubt on the output of the Genome Indexing, I have used the STAR program along with genome .fasta file and GFF file.

Genome size is 3GB, here is the file output

chrLength.txt
chrNameLength.txt
chrName.txt
chrStart.txt
genomeParameters.txt


I have another small Genome 60MB in size, I did the genome indexing, here is the file output

chrLength.txt
chrNameLength.txt
chrName.txt
chrStart.txt
exonGeTrInfo.tab
exonInfo.tab
geneInfo.tab
Genome
genomeParameters.txt
SA
SAindex
sjdbInfo.txt
sjdbList.fromGTF.out.tab
sjdbList.out.tab
transcriptInfo.tab


My point here is that, why I got the extra information for my small genome size, but I didn't get the same for the big size genome. I do apply the same procedure for the both.

here is the below information. Only difference I made for the large Genome size is (--sjdbOverhang 99 --genomeChrBinNbits 15) to reduce the memory, but the rest of things are same for small genome.

#!/bin/bash
mkdir DB
STAR --runMode genomeGenerate --genomeDir DB \
--runThreadN $NUM_THREADS \ --genomeFastaFiles XL9_2.fa \ --sjdbGTFfile XENLA_Frog.gtf+gff3 \ --sjdbOverhang 99 \ --genomeChrBinNbits 15  Could anyone give an idea, why there is different, I am new to this field, so I am wondering about the difference in this. Thanks in advance. Cheer San • The files missing in the case of the larger genome are the actual index itself - it doesn't look like STAR completed. Do you have STDOUT/STDERR from the runs? – sjcockell Jul 25 '18 at 13:20 • Here is my below syntax, I use it for It #!/bin/bash module load star/2.5.0c NUM_THREADS=22 mkdir Sangv92db STAR --runMode genomeGenerate --genomeDir Sangv92db \ --runThreadN$NUM_THREADS \ --genomeFastaFiles /ifs/home/skm9/san/xlaevis/XL9_2.fa \ --sjdbGTFfile /ifs/home/skm9/san/xlaevis/XENLA_9.2_Xenbase.gff3 --sjdbOverhang 99 \ --genomeChrBinNbits 15, It run and gene the files out same like the above I mentioned. – San Jul 25 '18 at 14:43
• here is the memory allocation I used for it, still not able to complete the indexing, ... qsub -pe threaded 4-20 -hard -l mem_free=400G -l h_vmem=560G -l mem_token=80G RunSTARIndex2.sh... – San Jul 25 '18 at 14:47