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?
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.
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
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).