Question: Fastq_Screen Does Not Detect Any Of The Contaminants
0
gravatar for roll
5.0 years ago by
roll240
United Kingdom
roll240 wrote:

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?

qc fastqc • 1.6k views
ADD COMMENTlink written 5.0 years ago by roll240
2

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

ADD REPLYlink written 5.0 years ago by Dan D6.6k

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.

ADD REPLYlink written 5.0 years ago by roll240

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

ADD REPLYlink written 5.0 years ago by Torst880
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