Reference genome for BOWTIE2

Question

[Arindam Ghosh]

I was working on EBI: Next Generation Sequencing Practical Course. Here in the first step to align the RNA-Seq data to the genome using BOWTIE2 we need a reference genome. The reference genome as I found comes as fragmented fasta file for each chromosome. I guess we need a combined file; where do I get it? Or is there a method to concatenate each file?

[Sej Modha]

Bowtie2 is compatible with multiple reference fasta file. It should work just fine with the reference file you have downloaded.

[Arindam Ghosh]

Multiple reference fasta file? So do I need to list the names of all the files containing each individual chromosome.

[Sej Modha]

The reference genome as I found comes as fragmented fasta file for each chromosome

is same as multiple sequences in a fasta file. Apologies for poor choice of terminology.

[GenoMax]

You can concatenate the files together with a simple cat *.fa > /path_to/new.fa command (putting the combined file someplace else so the command would not try to include it in the original cat).

[Arindam Ghosh]

Well I guess I found a way out. The database also contains something called Top-level sequence and Primary Assembly that is actually supposed to be used.