Question

Intron/Exon structure by cDNA SRA file

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9.3 years ago

Sebastian Obermaier ▴ 40

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

genome alignment RNA-Seq • 2.0k views

ADD COMMENT • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by Sebastian Obermaier ▴ 40

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What is in SRA? Are the reads aligned?

ADD REPLY • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by Sean Davis 27k

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As far as I can tell they are not.

ADD REPLY • link 9.3 years ago by Sebastian Obermaier ▴ 40

Ram · Answer 1 · 2015-08-10

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9.3 years ago

Sean Davis 27k

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

ADD COMMENT • link updated 5.1 years ago by Ram 44k • written 9.3 years ago by Sean Davis 27k