bowtie index location question

martinobarenco · 02-09-2010, 03:14 AM

Dear all,

when I type the command:

~/where/my/data/is $ bowtie -a -v 2 hg19 -c GTTCGATGAAATCTTCTTTTTCTGTTTTCACTTGGG

the following message is returned:

Could not locate a Bowtie index corresponding to basename "hg19"
Command: bowtie -a -v 2 -c hg19 GTTCGATGAAATCTTCTTTTTCTGTTTTCACTTGGG

whereas it works fine when run from the directory where bowtie actually is. I am a bit loth copying the data where the program is, so is there a way to specify the bowtie index(es) path?

Many thanks,

Martino

manoj123 · 02-09-2010, 03:33 AM

Hi Martino,

You can try absolute path of the index like below

~/where/my/data/is $ bowtie -a -v 2 /location/of/index/hg19 -c GTTCGATGAAATCTTCTTTTTCTGTTTTCACTTGGG

your index (.ebwt files) must be at /location/of/index/hg19.*.ebwt

martinobarenco · 02-09-2010, 04:54 AM

Thanks for the prompt answer, it works. It works also with the relative path (which I had tried initially), but the full path has to be specified. ie the path to the location of the executable is not enough.

martinobarenco · 02-09-2010, 05:46 AM

alternatively one can specify the path in the BOWTIE_INDEXES environment variable. I did that by adding the line below in the .bashrc file:

export BOWTIE_INDEXES=absolute/path/to/bowtie/indexes

then the path does not need to be repeated in the bowtie command.

(actually, this is well documented in the bowtie manual but the n00b that I am could not figure that one out)

02-09-2010, 03:14 AM	#1
martinobarenco Junior Member Join Date: Jan 2010 Location: London Posts: 3	bowtie index location question Dear all, when I type the command: ~/where/my/data/is $ bowtie -a -v 2 hg19 -c GTTCGATGAAATCTTCTTTTTCTGTTTTCACTTGGG the following message is returned: Could not locate a Bowtie index corresponding to basename "hg19" Command: bowtie -a -v 2 -c hg19 GTTCGATGAAATCTTCTTTTTCTGTTTTCACTTGGG whereas it works fine when run from the directory where bowtie actually is. I am a bit loth copying the data where the program is, so is there a way to specify the bowtie index(es) path? Many thanks, Martino

02-09-2010, 03:33 AM	#2
manoj123 Junior Member Join Date: Dec 2009 Location: London Posts: 2	Hi Martino, You can try absolute path of the index like below ~/where/my/data/is $ bowtie -a -v 2 /location/of/index/hg19 -c GTTCGATGAAATCTTCTTTTTCTGTTTTCACTTGGG your index (.ebwt files) must be at */location/of/index/hg19..ebwt** Last edited by manoj123; 02-09-2010 at 03:39 AM.

02-09-2010, 04:54 AM	#3
martinobarenco Junior Member Join Date: Jan 2010 Location: London Posts: 3	Thanks for the prompt answer, it works. It works also with the relative path (which I had tried initially), but the full path has to be specified. ie the path to the location of the executable is not enough.

02-09-2010, 05:46 AM	#4
martinobarenco Junior Member Join Date: Jan 2010 Location: London Posts: 3	alternatively one can specify the path in the BOWTIE_INDEXES environment variable. I did that by adding the line below in the .bashrc file: export BOWTIE_INDEXES=absolute/path/to/bowtie/indexes then the path does not need to be repeated in the bowtie command. (actually, this is well documented in the bowtie manual but the n00b that I am could not figure that one out)