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Old 09-25-2012, 10:47 AM   #1
ugolino
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Post bacterial RNA-seq mapping to draft genome

Hi there,

I have DNA and RNA-seq data from pathogenic E. coli, on Illumina GA-IIx, 68 bp PE reads. There is no complete genome for the strains I used. Although several genomes from closely related strains have been closed, they vary in phage content. I am wondering if there is an assembler that will allow mapping of RNA-seq reads to a draft genome?

Sorry if this has already been covered, I have not found a thread.

Many thanks for your insight!
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Old 09-25-2012, 12:55 PM   #2
swbarnes2
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Quote:
Originally Posted by ugolino View Post
Hi there,

I have DNA and RNA-seq data from pathogenic E. coli, on Illumina GA-IIx, 68 bp PE reads. There is no complete genome for the strains I used. Although several genomes from closely related strains have been closed, they vary in phage content. I am wondering if there is an assembler that will allow mapping of RNA-seq reads to a draft genome?

Sorry if this has already been covered, I have not found a thread.

Many thanks for your insight!
Bacteria have virtually no introns. You can map RNA reads to a reference genome just like you would a DNA experiment.

Also, your nomenclature is a little confusing. People in Next Gen usually mean "assemble" to mean de novo, with reads only, no reference genome. "Mapping" is when you use a reference genome.
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Old 09-25-2012, 01:11 PM   #3
ugolino
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Thanks for the reply!

Perhaps I did not explain well. The strain that I'm using has a phage that is not present in the complete genomes of closely related strains. Hence mapping to those complete genomes will not work. I have assembled de novo a draft genome of that strain and would like to know if I there is a short read aligner that can map the RNA reads to those de novo assembled contigs.
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Old 09-25-2012, 03:49 PM   #4
swbarnes2
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Originally Posted by ugolino View Post
Thanks for the reply!

Perhaps I did not explain well. The strain that I'm using has a phage that is not present in the complete genomes of closely related strains. Hence mapping to those complete genomes will not work. I have assembled de novo a draft genome of that strain and would like to know if I there is a short read aligner that can map the RNA reads to those de novo assembled contigs.
Any short read aligner will align to whatever reference you give it. Some will crash if any contig is shorter than your reads, so you might want to filter those out.
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Old 11-13-2013, 03:45 AM   #5
a3047886
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Default Draft genome alignment with NGS reads

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Originally Posted by swbarnes2 View Post
Any short read aligner will align to whatever reference you give it. Some will crash if any contig is shorter than your reads, so you might want to filter those out.
Hi there,

I am hoping to use Hiseq to do mRNA sequencing for an organism that has only a draft genome at the moment. Just to confirm from your previous post, if I use Galaxy to upload my NGS reads and then try to align these to the draft genome, this should work ok (being sure to filter any short contigs)?

Many thanks for your help.
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