text: user1075: I wish to use Rascaf to scaffold a fragmented draft genome.
  For this, I need to provide a BAM file of aligned RNA-seq reads and the draft genome.
  So, I indexed the draft genome with STAR like this:
  STAR --runMode genomeGenerate --genomeDir output/index --genomeFastaFiles draft.fa
  
  Then, I tried to aligned the reads like this:
  STAR --genomeDir output/index --readFilesIn reads.fastq.gz --readFilesCommand gunzip -c --outFileNamePrefix output/alignment --quantMode GeneCounts --outSAMunmapped None --outSAMtype BAM SortedByCoordinate --outSAMattrRGline ID:RG1 CN:yy \"DS: z z z\" SM:sample
  
  The latter commands outputs the following error:
  Transcriptome.cpp:51:Transcriptome: exiting because of *INPUT FILE* error: could not open input file exonGeTrInfo.tab
  Solution: check that the file exists and you have read permission for this file
            SOLUTION: utilize --sjdbGTFfile /path/to/annotantions.gtf option at the genome generation step or mapping step
  
  It suggests I should use a GTF file. But this is a draft genome of an individual for which no GTF is available. I could try to adapt a GTF from a close relative but for the scaffolding, it seems superfluous. Is there a way I can map with STAR without the GTF?
  These commands were run on a GNU/Linux machine.
  
  user1269: I don't think you can use the --quantMode GeneCounts option with no annotations. I think the error is trying to look for an exon file generated from the annotations to do the quantitation on. Remove that and I think it should work, as the manual specifically states that annotations are optional but highly recommended.
  
original_text: 1075: <p>I wish to use <a href="https://github.com/mourisl/Rascaf" rel="nofollow noreferrer">Rascaf</a> to scaffold a fragmented draft genome.</p>
  <p>For this, I need to provide a BAM file of aligned RNA-seq reads and the draft genome.</p>
  <p>So, I indexed the draft genome with STAR like this:</p>
  <pre><code>STAR --runMode genomeGenerate --genomeDir output/index --genomeFastaFiles draft.fa
  </code></pre>
  <p>Then, I tried to aligned the reads like this:</p>
  <pre><code>STAR --genomeDir output/index --readFilesIn reads.fastq.gz --readFilesCommand gunzip -c --outFileNamePrefix output/alignment --quantMode GeneCounts --outSAMunmapped None --outSAMtype BAM SortedByCoordinate --outSAMattrRGline ID:RG1 CN:yy \&quot;DS: z z z\&quot; SM:sample
  </code></pre>
  <p>The latter commands outputs the following error:</p>
  <pre><code>Transcriptome.cpp:51:Transcriptome: exiting because of *INPUT FILE* error: could not open input file exonGeTrInfo.tab
  Solution: check that the file exists and you have read permission for this file
            SOLUTION: utilize --sjdbGTFfile /path/to/annotantions.gtf option at the genome generation step or mapping step
  </code></pre>
  <p>It suggests I should use a GTF file. But this is a draft genome of an individual for which no GTF is available. I could try to adapt a GTF from a close relative but for the scaffolding, it seems superfluous. Is there a way I can map with STAR without the GTF?</p>
  <p>These commands were run on a GNU/Linux machine.</p>
   1269: <p>I don't think you can use the <code>--quantMode GeneCounts</code> option with no annotations. I think the error is trying to look for an exon file generated from the annotations to do the quantitation on. Remove that and I think it should work, as the manual specifically states that annotations are optional but highly recommended.</p>
  