Metagenomics data analysis

Question

[hafiz.talhamalik]

I have single end fastq file of metagenomics data. Can any one help me how to proceed with the data analysis of this data ? I have soil samples and I want to perform OTU, alpha diversity and Beta Diversity analysis on my data..!!

[natasha.sernova]

See this post, it looks useful.

When paired end reads doesn't join, can i consider them single-end in metagenomic analysis?

[hafiz.talhamalik]

@natasha.sernova The link is not related to my query. I have single end fastq file and the link you referred to is focused on merging pair-end files

[Friederike]

Can you elaborate and mention specific questions you have? What's the biological question of interest that you have? And what do you already know about general metagenomics data processing?

Answer 1

[GenoMax]

Have you looked at Qiime tutorials ( http://qiime.org/tutorials/processing_illumina_data.html )?

[hafiz.talhamalik]

Yes I have. but it's too complex to understand.. Is there any other option ?

[Joe]

Qiime is pretty much the de facto standard in this area, at least to my knowledge. If you wish to publish it, and I was a reviewer, I think you’d need a good reason not to use it.

[karthikqk95]

QIIME needs a mapping file to proceed with every step, what if i have trimmed reads doesn't know the Barcode as well as the Linker sequence which are essential to Qiime mapping file isn't it??

[hafiz.talhamalik]

you can also proceed without mapping file as well

[hafiz.talhamalik]

you can also proceed without mapping file as well

[Benn]

If it is too complex to understand, another option might be to search for collaborators.

[Friederike]

What exactly do you find too complex? The technical details of how to run the tool? Or its application, i.e. why you need to do certain processing steps? If the latter case is true, I recommend you modify your question to something like "Advice for useful introductory material on metagenomics analyses" or the like including a description of your background, i.e. what you already know about NGS data processing in general.