Bowtie: Indexing All Chromosomes In One Go

Question

[Click downvote]

I have downloaded the Rattus Norvegicus genome, which I will be analyzing. Building an index for it is not too hard, but is it possible to do all 21 of them in one go? i.e. is there a shortcut for

./bowtie-build /chromFa/1/chr1.fa rattus_norvegicus1
./bowtie-build /chromFa/2/chr1.fa rattus_norvegicus2
..
./bowtie-build /chromFa/20/chr20.fa rattus_norvegicus20

Bonus question: is it possible to have all the chromosomes for rattus_norvegicus indexed in one file? I imagine that I will want to search the whole genome, not just a particular chromosome.

This is so I could just write:

./bowtie -c rattus_norvegicus GCGTGAGCTATGAGAAA

instead of

./bowtie -c rattus_norvegicus1 GCGTGAGCTATGAGAAA
..
./bowtie -c rattus_norvegicus20 GCGTGAGCTATGAGAAA

Thanks.

PS. Why isn't the Y chromosome included in the chromosome chromFa.tar.gz (http://hgdownload.cse.ucsc.edu/goldenPath/rn4/bigZips/)? Mistake or what?

Answer 1

[matted]

Bowtie can index a FASTA file with multiple sequences (chromosomes in it). So you should do something like cat chr*.fa > all.fa and index all.fa.

The main Bowtie site has prebuilt indices for rat (rn4), which might save you some time.

Not sure about the rat Y chromosome. If I had to guess, I'd say it's incompletely sequenced/assembled.

[Click downvote]

Thanks. So fasta files can be appended and no harm is done? But will bowtie tell me which chr the sequence I'm looking for is on if all fa files are appended? Will this zero-index each and every chromosomes or are they all put together such that 0 means first bp on chromosome one and last index is the last bp on the last chromosome?

[matted]

Yes / yes / yes / no. It works how you'd want it to; this is how everyone uses it.