How To Extract Data From Exel Sheet

Question

[sebabiokr]

Greeting to all,

I have analyzed my Metagenome data in MG RAST pipeline. There is much information about the organism in the table. Could you please tell me how to extract those data to simple table format to discuss the results?

Thank you

Sebastian

EDIT

The date contains following information

metagenome source domain phylum class order family genus species abundance avg eValue avg % ident avg align len# hits i used RDP as a annotation source. i need to extract all RNA data and need to classify them in %.

Thank you

[Neilfws]

Without some idea of (1) what the data look like and (2) what kind of analyses you want to do - no, we cannot. Please provide more detail.

[Neilfws]

Please edit the original question with this information, rather than posting it in an answer. I have made a start for you, but you need to make it readable.

[sebabiokr]

Thank you i will do the same.

[Whetting]

could you include an example of the input and desired output? Do you have any preferences in coding language used?

Answer 1

[Josh Herr]

So you uploaded FASTA files into MG-RAST and now have an excel file output? You probably have a table of data from MG-RAST and you need to know what to do with it? Why did you sequence your samples in the first place if you have no understanding of your research question or what you will do with your data output?

By adding your sequences to the MG-RAST pipeline, did you actually analyze the data or did you use the default settings on the pipeline for FASTA annotation? You say you used the RDP database, does that mean you have amplicon data? If you have WGS data you will have to use another database for annotation (MG-RAST uses the M5NR database as standard now).

You give a list of the output for the columns of your TSV table, but you do not say how these columns were computed by the pipeline. In MG-RAST there are four options that will provide you a table like this: organism abundance ((1) representative/best hit and (2) lowest common ancestor) and functional abundance ((3) hierarchical and (4) complete annotations). Which one did you choose? Also, you are not describing the entire table so I do not know if you actually analyzed the data properly or don't know how to see all the columns on your table.

Your table annotations are the following: - metagenome - your sample name - source - your treatment - domain - domain of closest BLAT hit - phylum - phylum of closest BLAT hit - class - do I need to go on here? - order - family - genus - species - abundance - read abundance for this organism/gene - avg eValue - the average eValue for all the hits (this will vary often at the level of clustering in your pipeline, typically at 95% to 98% for OTUs) - avg % ident - the average % match of your reads to the database hit - avg align len - the average length of your sequence alignment - # hits - number of hits to the database (can be, and usually is, different from the read abundance)

Lastly, you say you need to "extract RNA data" what does this mean? Do you have metagenomic transcriptome cDNA library data or are you confused and looking for ribosomal DNA profiles?

There are many different directions to take from where you are at now. Do you know what type of analyses you will be using to assess your metagenomic (or amplicon) data? You'll have to figure this out.

Please in the future, provide us with enough information to help you, but first, read the manual or instructions, or take a basic course, before asking help in a forum like this.

Answer 2

[vaskin90]

Export the table to Comma Separated Value format. Excel can do that. Then a lot of tools can read it.

[Josh Herr]

This question is referring to the spreadsheet from within MG-RAST, which is already in TSV format, but yes, lots of tools can read either a TSV or CSV formatted data matrix.