Question: Intron/Exon structure by cDNA SRA file
1
gravatar for Sebastian Obermaier
3.7 years ago by
Germany
Sebastian Obermaier10 wrote:

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

rna-seq alignment genome • 1.1k views
ADD COMMENTlink modified 3.7 years ago by Sean Davis25k • written 3.7 years ago by Sebastian Obermaier10

What is in SRA?  Are the reads aligned?  

ADD REPLYlink written 3.7 years ago by Sean Davis25k

As far as I can tell they are not.

ADD REPLYlink written 3.7 years ago by Sebastian Obermaier10
0
gravatar for Sean Davis
3.7 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

If you have a "reference" genome against which to align and your transcriptome reads from SRA, you can:

  1. use the fastq-dump command from the SRA SDK 
  2. Align the reads with STAR or HISAT to your genome
  3. Examine the resulting output files and BAM files in the region of your gene

 

ADD COMMENTlink written 3.7 years ago by Sean Davis25k
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