index reference file to use for bowtie

[swang129]

I am trying to run Bowtie on a small test fastq file. It is human hg19 build. I found that the index file can be downloaded from the right panel of this:

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

The downloaded files are:

hg19.1.bt2
hg19.2.bt2
hg19.3.bt2
hg19.4.bt2
hg19.rev.1.bt2
hg19.rev.2.bt2
hg19.zip
make_hg19.sh

make_hg19.sh requires bowtie2. and I don't have authorization to install bowtie2 onto our server.

Since hg19 must be a very common reference, is there anyplace that we can directly download the indexed file of hg19? what is the appendix for this index file?

thanks

[Jeremy]

Bowtie(1) needs a Bowtie(1) library, it can't use a Bowtie2 library. Assuming you already have Bowtie installed then make the library using the 'bowtie-build' command. You should upgrade to bowtie2 though, it is much better.

[swang129]

Thanks I see