Bowtie -S output error

[mln]

Hi everyone,

I'm trying to generate an alignment using bowtie, and my output is supposed to be a .sam file. My command is

bowtie -x complete-genome -1 treat_1.fq -2 treat_2.fq -S output_treat.sam

The problem is I keep getting an error saying "could not locate a bowtie index corresponding to base name 'output_treat.sam'".

Any suggestions would be hugely appreciated. I'm completely new at this and my command line troubleshooting skill is still being developed.

[mastal]

what version of bowtie are you using?

If you are using a version of Bowtie2, I think that should be an uppercase -X for the index.

[yueluo]

Try :
bowtie complete-genome -1 treat_1.fq -2 treat_2.fq -S output_treat.sam

[mln]

Thanks, yueluo! That seemed to do the trick.

mastal, the VM isn't recognizing the bowtie2 command. When I try bowtie2 the machine asks me to correct it to bowtie. Looking back through the manual I think you are right about the uppercase, though.