Intron/Exon structure by cDNA SRA file
Hello everyone,
I'm trying to predict the exact intron/exon structure of a gene of interest. Available I have the genomic sequence and the transcriptome of the organism at NCBI's SRA. I tried it using the SRA BLAST tool provided at NCBI but I can't seem to get it right. Is there a simple way to assemble the short reads with the template of the genomic DNA? I just need to do this process with one gene.
Thanks in advance
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Sebastian Obermaier •
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Sebastian Obermaier •
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If you have a "reference" genome against which to align and your transcriptome reads from SRA, you can:
- use the fastq-dump command from the SRA SDK
- Align the reads with STAR or HISAT to your genome
- Examine the resulting output files and BAM files in the region of your gene
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Sean Davis
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What is in SRA? Are the reads aligned?
As far as I can tell they are not.