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 NUM_THREADS=12 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.