I have a *.fasta file through nanopore sequencing (Min Ion) of approx ~250MB. I'm having problem in its analysis via MEGA Software due to large file size. I need to select a particular bacterial sequence out of it and then draw phylogenetic tree of particular bacterial sequence for further analysis.
Kindly help!
First, I am not sure it is really a fasta file or not. Because the final result from Nanopore is usually *.fastq file. Or did you get the contigs from your bacteria after denovo assembly. You can check whether it is fasta or fastq format by observing several lines from your file (In linux, if your file named a.fasta --> command: head a.fasta # it will print first 10 lines of your files).
In case of actual *.fasta, with the size ~ 250Mb. I think you can use some text editors (like Notepad or Sublime) to read it. Hope it work!
The analysis could work as follows:
1. Use an alignment editor (e.g. Align by SequentiX, https://www.sequentix.de).
2. Load the file.
3. Perform an alignment.
4. Select the desired samples/species and export the data into a file format for phylogenetic analysis (Mega, PHYLIP, MrBayes, etc.).
5. Analyse the data and construct a phylogenetic tree using a phylogenetic analysis software (see above).
Agree with Vo, the Output file of nanopore Is FASTAQ.
choice of analysis:
https://nanoporetech.com/nanopore-sequencing-data-analysis.
text editor will reduce the size.
Sir@ we have already converted fastq file to fasta format. Kindly provide the suggestions for steps ahead. Now the problem that we are facing is identification at species level, whatever the phylo tree is showing is unknown abcd....1234.... type alphabets only (shown in attachments). Pls provide suggestions.
Vo phuoc Tuan Hatem Zayed
Perhaps, this are the labels as provided by the FASTA file? Open the FASTA file with any text editor (e.g. notepad.exe) and check. The tree can only show the sample names as given in the FASTA file.
Anwesh Pandey
Few important points
- Its almost impossible / useless to use a file of 250 Mb for phylogenetic inference = does not make sense. Sounds like several tens of genomes are present in your fasta file. It is definitely not the way to go for phylogenetic analysis
- What kind of sequencing have you done, what is your data type?
- If you want to select any particular sequence, which means "one" sequence, how will you make a tree with one sequence?
- If you are only interested in one or few sequence, why would you make a phylogenetic tree in first place? There are several other ways to do that job.
I would strongly recommend you to think and confirm what you are doing and what you want to do. If you have sequences, just making a phylogenetic tree is not a good idea. Generally you don't make phylogenetic tree, just because you have sequences on your hand and you can make a tree, unless you are interested to infer something by a phylogenetic tree.
All other things like fasta or fastq or checking what is in file is just secondary thing.
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