text: user3113: 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.
  Cheer
  San
  
  user77: You didn't get extra information with the small genome, the index for the larger one just wasn't made. My guess is that you ran out of RAM. For mammalian sized genomes ensure you have at least 30GB of RAM, likely more like 60GB. Also, make sure to look for error messages.
  
original_text: 3113: <p>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.</p>
  
  <p>Genome size is 3GB, here is the file output</p>
  
  <pre><code>chrLength.txt
  chrNameLength.txt
  chrName.txt
  chrStart.txt
  genomeParameters.txt
  </code></pre>
  
  <p>I have another small Genome 60MB in size, I did the genome indexing, here is the file output</p>
  
  <pre><code>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
  </code></pre>
  
  <p>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.</p>
  
  <p>here is the below information. Only difference I made for the large Genome size is (<code>--sjdbOverhang 99 --genomeChrBinNbits 15</code>) to reduce the memory, but the rest of things are same for small genome.</p>
  
  <pre><code>#!/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
  </code></pre>
  
  <p>Could anyone give an idea, why there is different, I am new to this field, so I am wondering about the difference in this.</p>
  
  <p>Thanks in advance.</p>
  
  <p>Cheer
  San</p>
   77: <p>You didn't get extra information with the small genome, the index for the larger one just wasn't made. My guess is that you ran out of RAM. For mammalian sized genomes ensure you have at least 30GB of RAM, likely more like 60GB. Also, make sure to look for error messages.</p>
  