The file "microbial_community.trimmed.fastq.gz" contains the fastQ reads of a known microbial community. A targeted approach was chosen to study the microbial composition: full-length 16S rRNA gene was amplified by PCR and sequenced using Oxford Nanopore technology (1,2). Sequencing adapters and PCR primers were removed using the tool cutadapt (3).
Please answer the following questions:
Question_1: How many reads are in the dataset? What's the average read quality? and the average length?
Question_2: Are there any "off target" reads (ex. longer or smaller fragments)? If yes, remove them from the dataset.
Question_3: Would you include a chimera detection step? Justify your answer
Question_4: What are the 10 most abundant microbial species?
Question_5: Provide further details about the analysis pipeline used
Sincerely,
Oleg
Welcome to Biostars artemchuki :). I recommend you to try to explain your task in the question and your attempt to solve it. The chances of having a useful response are higher. In addition, you never know who else is out there struggling with the same issue that would also benefit from your question.
This is task
The file "microbial_community.trimmed.fastq.gz" contains the fastQ reads of a known microbial community. A targeted approach was chosen to study the microbial composition: full-length 16S rRNA gene was amplified by PCR and sequenced using Oxford Nanopore technology (1,2). Sequencing adapters and PCR primers were removed using the tool cutadapt (3).
Please answer the following questions: Question_1: How many reads are in the dataset? What's the average read quality? and the average length?
Question_2: Are there any "off target" reads (ex. longer or smaller fragments)? If yes, remove them from the dataset.
Question_3: Would you include a chimera detection step? Justify your answer
Question_4: What are the 10 most abundant microbial species?
Question_5: Provide further details about the analysis pipeline used
fastq file I will send by email
Biostars is not a site for getting homework/other assignments done by someone else. If you have specific questions then post those.
This is no homework or assignment. This is done to understand how to make analysis, but there is not explanation. There are results, but how it was done?
If someone did this analysis for you then you should ask them about specifics. We have no way of telling you what tools may have been used.
This is just to understand what tools to use.
Have you used google search to find prior threads on biostars? (tip add
site:biostars.orgwhen you search via google to limit the search to biostars site)? You should be able to find answers for most of your questions that way. If you need specific clarification then ask.e.g. You can use a tool like
nanoplot(LINK) to answer your question 1.Helpis not a relevant tag - remove it.I've done the necessary edit myself as you did not do it properly. This does look like an assignment, so we cannot help you with that. If you run into specific problems while addressing these questions, please feel free to ask us.