Fastq_Screen Does Not Detect Any Of The Contaminants

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10.5 years ago

roll ▴ 350

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?

fastqc qc • 2.7k views

ADD COMMENT • link 10.5 years ago by roll ▴ 350

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

ADD REPLY • link 10.5 years ago by Dan D 7.4k

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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 REPLY • link 10.5 years ago by roll ▴ 350

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

ADD REPLY • link 10.5 years ago by Torst ▴ 980

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