Questions about how to set '--output prefix'

[sunbacteria]

Hi! I want to use ExpansionHunter to find specific STRs in our bam files. However, I am not familiar with the codes.

I noticed that in the given example, it writes:'--output-prefix output/repeats' In my own script, i change it to '--output-prefix ' I am not sure if I make it right. After I tried to run this script, it comes out that '--output-prefix' is required but missing and there is also an error report that "--output-prefix: command not found".

I wondered where i got it wrong.

Thanks!

[egor-dolzhenko]

Apologies for the late reply! Could you please confirm that there are no spaces after the \ character on the second line from the bottom? If there is a space, \ would not escape the end of the line and your shell will interpret --output-prefix as a separate command (which will lead to "--output-prefix: command not found" error).

[GabevandenHoeven]

Hello!

I am trying to do the same thing and I am running into a similar problem. The only thing that is different is that with me it says: [the option '--output-prefix' is required but missing]. I also don't know what the issue could be, though I can confirm that there is no space after the "\" in my code.

Thanks!

[egor-dolzhenko]

Thanks for the question! Could you please copy/paste the exact command you are using?

[GabevandenHoeven]

Hello, thanks for your quick reply! As I was writing this someone noticed that one of the dashes was a windows character. This turned out to be the issue for me.

[egor-dolzhenko]

Glad to hear that you were able to resolve the issue!