Does anybody know what is the best and trustable way to concatenate different FASTA files for making them index together?
thanks in advance
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lkianmehr
Just cat them together. I am not sure what you mean by trustable?
If you have spaces in the headers (e.g. words separated by names) make sure to change the space to _. Most aligners will drop things past first space when reporting alignments (e.g. bbmap is an exception and will keep the entire name by default unless you use trd=t). You may get confusing results if the part of name up to first space is common to more than one record.
As Genomax commented :
In a unix shell :
cat file1.fasa file2.fastq file3.fasta > merged_file.fasta
or even easier if all your fasta files are in a directory and ends by .fasta
cat *.fasta > merged_file.fasta
I tend to remember that there were cases (also reported here on Biostars) when cat *.fasta somehow caused an infinity loop because the output file would be constantly appended to itself (as it also ends on .fasta). To avoid this, consider to use:
find . -maxdepth 1 -name \*.fasta | xargs cat > output.fasta
that's a good point !
How do i delete all the fasta files with my info
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How do i delete all the fasta files with my info
Please ask a new question and give us as much information as you can. Do not add an answer unless you're answering the top-level post. I'm moving your "answer" to a comment and deleting the other duplicate "answer".
In this it would be "please give any information"...
nadiawerksfoon imagine you were in the situation of a user reading this and willing to help, could you reproduce at all what the problem is? At least I cannot. Probably others cannot as well. Add details!