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Old 04-14-2015, 10:07 AM   #1
vitor
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Default How analyze DNA's reads by HiSeq-2000?

I need to analyze reads of viral DNA by deep sequencing using HiSeq-2000. I'll check the substitutions throughout the genome and identify the viral virants, but i don't know what package or scripts to use. Do you have any suggestions, friends?

Thanks.
Vitor
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Old 04-14-2015, 10:29 AM   #2
jwfoley
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What kind of data do you have so far ("raw" FASTQ or is it already processed?) and what exactly do you want to achieve?
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Old 04-14-2015, 10:38 AM   #3
vitor
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jwfoley, the data's still being processed and I'll receive in FASTQ. I want to find mutation hot spots, nucleotide substituations and comparing the diversity of the genome at various times.
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Old 04-14-2015, 10:39 AM   #4
diego diaz
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Hi vitor,

First, you need to trim your reads, to discard low quality bases. You could use Trimmomatic, fastx_toolkit, prinseq, etc. Then, you have to map your sequences to the reference genome. If you want to analyze substitutions, I think it is more suitable to chose a more sensitive mapper, as SMALT, but your reads should be short (75 bp) , because they were sequenced with HiSeq, in this case I think bowtie 1 is good enough, Once you have your reads mapped, you have to perform a SNP calling. I recommend you freebayes, because it allows to analyze haploid organisms. With your VCF file generated with freeBayes you can perform a functional analysis with SNPeff.

I hope it helps!

Last edited by diego diaz; 04-14-2015 at 10:48 AM.
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bioinformatics help, dna, mutation/variant base, ngs analysis, virus

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