Reads not getting mapped to reference genome
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2.4 years ago

My sequence data have 3 16srRNA, each belonging to 3 different organism. When I map the paired end reads to the reference genomes of the three organism, using mappers like Bowtie and Bowtie2, it is not showing any hits to the reference genome. Why is it that?

mapping Bowtie de novo assembly whole genome • 1.2k views
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Does your reference contain 16S RNA sequences? Sometimes rDNA repeats may not be included. Do they align if aligned directly to 16S reference?

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We are trying to build our own assembly ( de novo assembly) and not 16srRNA sequencing, but whole genome sequencing. And yes the reference genome do contain the 16S RNA sequence.

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If none of your reads are mapping any of the reference genomes (which is not an assembly problem) then you should test a few reads from your data by blasting them at NCBI to make sure you have the right data first (see what genome they hit, limit blast search to bacteria to make things simple).

For doing assemblies you can go de novo route (e.g. SPAdes) or reference based assemblies. That is a different type of analysis.

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When using bbmap they do get aligned to the 16s reference but when using bowtie again getting 0 mapping

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There can be many reasons, on top of my head 1. The reference is not complete, you can test this by blasting few reads. 2. Paste the Bowtie2 (don't use Bowtie) and let's see if they are too restrictive.

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yes I have tried with bowtie2 also but no hits found and also I am using complete reference genomes too.

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