Indexing of the reference for RNA-seq in S. meliloti

[Carmen]

Hello,
my question is about the indexing of the reference sequence against which to align our Illumina reads. For S. meliloti 1021 genome there are three fasta-format files and three annotation files available on NCBI (1 for the chromosome and 2 for the megaplasmids). Before to align our reads to the reference we have performed the indexing of each reference sequence by using bowtie2-build producing three reference index files. To make the alignment we need one index file. How we can combine the three files in one file?

Thanks in advance
Crm

[dpryan]

The bowtie2-build command allows you to specify multiple fasta files for indexing, you can do that or concatenate the fasta files prior to indexing.

[Carmen]

I will try the indexing with the specification of multiple fasta files

Many thanks
Crm