I have downloaded .fastqfiles from SRA and now trying to filter out reads aligning to ERCC spike ins, rRNA and Repetitive Elements (from RepeatMasker).

I would like to do this step by step, repeating the command on the unaligned results from the previous step using something like this:

bowtie2 -p 2 - N1 --un-conc <unaligned fastq> --al-conc <aligned fastq> \
    -1 <dowloaded mate1 fastq. -2 <downloaded mate 2 fastq> \
    -S <output alignment sam>

As I got from the manual, first I need to build .bt2 indices for each alignment (namely, for ERCC, rRNA, RepetitiveElements) How can I create indices for the aforementioned command and which data should I download for it?

Would be happy for any help!