Fastq_Screen Does Not Detect Any Of The Contaminants

Question

[roll]

I am running fastq_screen to pick up the contaminants from my fastq file.

The program runs successfully but finds no match. I have used the same data with FastQC and it finds some of the comtaminants in the same data.

Can anyone advise why fastq_screen can not find a match?

[Dan D]

what kind of contaminants are you looking for? Which databases do you have specified in your .conf file for the application?

[roll]

I am looking for the adapters/trimmers. I have the contaminant file from FastQC which I converted into fasta format and indexed it using bowtie. That is my in my .conf file.

[Torst]

You'll need to share the command line you typed, and your config file, before we can help you.