I've been trying to merge separate fasta files into a single file. I use
cat *.fasta > outputname but every time I do it I lose some of the headers, which is puzzling.
after using cat, output is:
>scaffold001 AGTCATGAT AGTATAAAA
There is no pattern, some random scaffolds headers appear, some don't. I have no duplicate scaffolds to merge, so that's not the case. I double checked and basically all names have the same format, with changes only in the numbers, there's no spaces or anything.
I have no idea what could be going on or what else I can use to concatenate the files.