fastq screen aligner no specified.

Question

[Ximena]

Hello, I´m new in NGS and I´m trying to run fastq screen but when I do it, it send me these message: "Aligner (--aligner) not specified. Did not find Bowtie/Bowtie2/BWA paths and/or index files Please check: you have provided the full path to the aligner INCLUDING the executable filename Please check: the specified genome indices comprises the full path AND the basename of the index files See documentation for further details" And I already changed the path and uncomment the aligners I want to use. In the configuration file it appears like this:

This is an example configuration file for FastQ Screen

############################
## Bowtie, Bowtie 2 or BWA #
############################
## If the Bowtie, Bowtie 2 or BWA binary is not in your PATH, you can set 
## this value to tell the program where to find your chosen aligner.  Uncomment 
## the relevant line below and set the appropriate location.  Please note, 
## this path should INCLUDE the executable filename.

BOWTIE /usr/bin/bowtie
BOWTIE2 /usr/bin/bowtie
BWA /usr/bin/bwa

I don´t know what to do in order to run it succesfully. Can someone please help me?

[GenoMax]

You need to change this configuration file to point it to the location where the aligner executable can be found.

So as an example following line in the config file

 /usr/bin/bowtie

may need to become

/home/user/bowtie/bin/bowtie

Just saying you want to use bowtie is not enough. You actually have to install that aligner. That said, what OS are you using? You will need to make sure that your OS has a version of the aligner binary that you can use.

[Ximena]

Thank u so much, my OS is linux. I will try your advice.