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..!!
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hafiz.talhamalik
Have you looked at Qiime tutorials ( http://qiime.org/tutorials/processing_illumina_data.html )?
Yes I have. but it's too complex to understand.. Is there any other option ?
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.
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??
you can also proceed without mapping file as well
you can also proceed without mapping file as well
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See this post, it looks useful.
When paired end reads doesn't join, can i consider them single-end in metagenomic analysis?
@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
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?
I have soil samples and I want to perform OTU, alpha diversity and Beta Diversity analysis on my data..!!
If Qiime is to complex at this moment you can take a look at this to get you started.
First:
https://www.drive5.com/usearch/manual/pipe_otus.html
Second:
https://www.drive5.com/usearch/manual/pipe_otutab.html
Third:
https://drive5.com/usearch/manual/cmd_beta_div.html
https://drive5.com/usearch/manual/cmd_alpha_div.html
Only to get you started, you will notice that there is more then one cluster method and many ways to filter your otus and and otu table which all have a big impact on the end result.
!