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I really don't catch what you are trying to do. Looking for contamination? Detect any problems during the librarie generation?
You may know on which organism your reads may map... so personnally, when I suspect a contamination, I first map my reads on my target genome with bowtie, asking to report all the NOT mapped reads in a file (using the --un parameter), then you have a "clean" fastq file to work with... You can make a fastqC on this file, it will tell you if you have some overrepresented sequences and their probable orgin (mostly if they are Illumina adapters).
If it's a contamination, you can ask the sequencing facility you did your sequences, which organisms were sequenced at the same time than your samples, which can already give you an idea... In my case, most of the observed contaminations (on mouse samples) were human (so most probably coming from the scientist preparing the sample, sic!!!).
s.
You may know on which organism your reads may map... so personnally, when I suspect a contamination, I first map my reads on my target genome with bowtie, asking to report all the NOT mapped reads in a file (using the --un parameter), then you have a "clean" fastq file to work with... You can make a fastqC on this file, it will tell you if you have some overrepresented sequences and their probable orgin (mostly if they are Illumina adapters).
If it's a contamination, you can ask the sequencing facility you did your sequences, which organisms were sequenced at the same time than your samples, which can already give you an idea... In my case, most of the observed contaminations (on mouse samples) were human (so most probably coming from the scientist preparing the sample, sic!!!).
s.
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