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Old 11-08-2012, 08:43 PM   #1
Location: Sydney, Australia

Join Date: Nov 2011
Posts: 24
Default Hiseq reads -assembly n mapping on a reference genome


Background: Got 5 genomes sequenced with the GA2, assembled n annotated them denovo using soapdenovo, velvet.. also mapped them on to a reference using soap aligner.. no problem. Then got another set sequenced using the Hiseq.. I think its a contamination problem as the genome size after assembly is way too big.

I got my sample genome sequenced using the Hiseq (100bp, per end).
quality trimmed it using dyanamic trim, assembled it via Soapdenovo and velvet and I was getting a genome size of 16mb, when it should be only 4mb. So I put it through Megan (a metagenome analyser) and finally got a genome thats around 4.8mb in size.I put that on RAST (Rapid annotation Subsystems Technology) for annotation.

OPTION2: Another approach, took the .fastq file after the dyanmic trim step n mapped it on my reference genome (using soapaligner), then extracted the reads (converted soap to sam, sam to bam and then used bam2fastq to extract the mapped reads. Now the mapped reads file is 5GB and I havent been successful in uploading it onto RAST. How do I find out the genome size of this genome, using the data from option 2? Also what else can I use to annotate the reads? I thought of putting it through megan again. Megan will separate out any contamination and give me only the sample strain sequences, which I can then put on RAST.

Please help. Any tips would be sooo appreciated.

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