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Old 07-31-2014, 04:35 PM   #1
swang129
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Location: Bay area

Join Date: Jun 2014
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Default index reference file to use for bowtie

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
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Old 07-31-2014, 05:29 PM   #2
Jeremy
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Location: Pathum Thani, Thailand

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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.
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Old 07-31-2014, 05:30 PM   #3
swang129
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Thanks I see
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