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-   -   Need Sequence Format Converter (http://seqanswers.com/forums/showthread.php?t=24281)

byou678 10-19-2012 01:32 PM

Need Sequence Format Converter
 
Hi All,

Could anyone recommend the Online Sequence Format Converter?

For example, I would like to convert sequence TXT file to FASTA file, or FASTA to FASTQ. After conversion, I need download it and then upload to some where else.

I really appreciate any response !!

mnkyboy 10-19-2012 01:35 PM

All you need to make a FASTA is to make a > on the first line.

http://en.wikipedia.org/wiki/FASTA_format

You cannot got from FASTA to FASTQ.

byou678 10-19-2012 01:45 PM

Thanks a lot for your reply!

After adding > on the first line in the TXT file, How can u save it to FASTA file (with .fasta extension)?

In addition, if there are Thousands of reads/sequences in my TXT file, so I need manually add Thousands of the <, respectively? Not easy :)

One link here:
http://sequenceconversion.bugaco.com...ogy/sequences/


Quote:

Originally Posted by mnkyboy (Post 87173)
All you need to make a FASTA is to make a > on the first line.

http://en.wikipedia.org/wiki/FASTA_format

You cannot got from FASTA to FASTQ.


mnkyboy 10-19-2012 01:49 PM

It is just a text file so save it as .fa or .fasta

If you need a fasta per sequence you will have to write a script, or use some sort of replace function. If you just want the whole file a fasta you just need to add the > at the beginning.

byou678 10-23-2012 12:02 PM

Thanks for your reply.
But i think we can convert FASTQ to FASTA, Any other response to confirm it?

Take a look at this link ( FASTQ to FASTA ):
https://app.bugaco.com//converter/bi...q_to_fasta.php


Quote:

Originally Posted by mnkyboy (Post 87173)
All you need to make a FASTA is to make a > on the first line.

http://en.wikipedia.org/wiki/FASTA_format

You cannot got from FASTA to FASTQ.


mbblack 10-23-2012 12:17 PM

Quote:

Originally Posted by byou678 (Post 87446)
Thanks for your reply.
But i think we can convert FASTQ to FASTA, Any other response to confirm it?

Take a look at this link ( FASTQ to FASTA ):
https://app.bugaco.com//converter/bi...q_to_fasta.php

Sure, since a FASTQ file is still just a text file containing sequence and quality data, you can parse out the sequence only data. But, you cannot take a simple FASTA file of sequences and make it a FASTQ file.


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