Would appreciate any advice/suggestions on the following task:
The sample was Illumina NGS sequenced for 16S amplicon and by WGS approach (I have fastq files for both). From 16S amplicon data, I have 400 nuc piece of 16S rRNA gene of bacteria which need to be analyzed by qPCR from the original sample. In the original sample these OTU is quite abundant - 15-20%. It would be nice to have a sequence of the whole 16S rRNA gene to be able to design several specific qPCR primers.
What could be the best strategy/software (is it possible at all?) to extract/re-construct the sequence information of the whole 16S rRNA gene from fastq files of WGS data? Any comments on a strategy of opening the fastq file in notepad and trying to do alignment and assembling starting from the known 400 nuc piece?
For WGS, assemble and annotate. Annotation will easily give you your gene. If not, you can use assembly with blast to get your gene.
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