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.