Question: Metagenomics data analysis
0
gravatar for hafiz.talhamalik
13 months ago by
Pakistan
hafiz.talhamalik230 wrote:

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..!!

data analysis metagenomics • 437 views
ADD COMMENTlink modified 13 months ago by WouterDeCoster43k • written 13 months ago by hafiz.talhamalik230

See this post, it looks useful.

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

ADD REPLYlink modified 13 months ago • written 13 months ago by natasha.sernova3.7k

@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

ADD REPLYlink written 13 months ago by hafiz.talhamalik230

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?

ADD REPLYlink written 13 months ago by Friederike5.7k
1
gravatar for genomax
13 months ago by
genomax83k
United States
genomax83k wrote:

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

ADD COMMENTlink written 13 months ago by genomax83k

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

ADD REPLYlink written 13 months ago by hafiz.talhamalik230
1

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.

ADD REPLYlink written 13 months ago by Joe16k

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??

ADD REPLYlink written 4 months ago by karthikqk950

you can also proceed without mapping file as well

ADD REPLYlink written 4 months ago by hafiz.talhamalik230

you can also proceed without mapping file as well

ADD REPLYlink written 4 months ago by hafiz.talhamalik230

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

ADD REPLYlink written 13 months ago by Benn8.0k

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.

ADD REPLYlink written 13 months ago by Friederike5.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1360 users visited in the last hour