Combine multiple fasta files in galaxy?

Question

[ando.kelli]

Hi there,

I have a few hundred fasta files that I need to combine into a single fasta file. I thought it would be a relatively straight forward thing to do in Galaxy, but is proving to be a bit of a pain.

I was hoping to do this in Galaxy as I don't have command line experience.

Anyone know of a way to do this in Galaxy?

[GenoMax]

You could do this in Windows (combining fasta files ) or linux/OS X (cat *.fa > new_dir/combined.fa).
If you want to do this in galaxy then perhaps this way: https://biostar.usegalaxy.org/p/8324/ (which may prove to be a huge pain).

Answer 1

[Peter]

The Galaxy concatenate datasets tool ought to work nicely here (assuming you don't have any bad FASTA files missing a trailing new line character), essentially the command line tool cat wrapped for use within Galaxy.

Answer 2

[ando.kelli]

Hi all,

I've ended up learning how to do all of my NGS analysis in a Linux environment (with some occasional text manipulation in Galaxy). For those who are daunted by the prospect like I was, I'd encourage you to get stuck in as it's made my life a lot easier (after an initial phase of constant Googling and confusion) :-) Github will be your best friend when looking for scripts/workflows.

To join the fasta files I did the following:

Make sure you are in the right directory (folder with your fasta files)

then:

cat *.fasta > combined.fasta

Using the * will combine all of the .fasta files in your current directory. If you don't want to join all of the files in the directory then be more selective like this:

cat fileone.fasta filetwo.fasta filethree.fasta > combined.fasta

you can also define where you want your output saved if you don't want it saved to the folder you're working in:

cat *.fasta > path/combined.fasta

Hope that helps :-)

Kel

[GenoMax]

Good for you. Now that you have learned the power of command line there is no going back :-)