<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>

CC BY-SA 4.0
2018-05-26T04:04:00.897Z
2018-05-26T04:04:00.897Z
Jared Andrews
<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>

<read-mapping><rna-alignment><genome-sequencing><scaffold>
Can I run STAR without an annotation file?
# Can I run STAR without an annotation file?

(Asked by: username_0 on 2018-05-25)

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.

**Tags:** read-mapping, rna-alignment, genome-sequencing, scaffold

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## 1 answers

### Answer by username_1 on 2018-05-26. Score: 3 | Accepted answer

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.


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