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.


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.


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.