While NGS QC, Why its bad to have similar sequences in the fastq file? Wouldn't it be normal to have more than one copy of the same read?

More Ahmad Ali's questions See All

Hello fellow researcher .. What is the meaning of your name?

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Can we classify HV and LV lines based on line length?

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Which is better medicine or food in obesity?

Preference in terms of the scientific aspect

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Is IMPACT FACTOR justified in case of Taxonomy?

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Can anyone share his experience regards Smoothing in origin?

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Is it possible to set a breakpoint at a specific DYNAMIC instruction using the GNU Debugger (GDB)?

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Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

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Runs of nucleotides in Sanger sequencing?

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Has anyone used the Illumina ITS1 primer sets?

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Errors in DNA sequences?

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I can detect my protein but the encoding DNA sequence has stop codons within. Should I ignore the stop codons?

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Repository for capture-seq raw reads?

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Péter Gyarmati

I guess you talk about RNA seq? It is not necessarily bad, but it is bad if those are PCR artifacts as this will bias your results. Eg

https://www.nature.com/articles/srep25533

Frank R Burns

It is normal to have overlapping reads, but the probability of have two independent reads start and stop at the same base if very low, so if multiple reads have identical starting and end bases it is taken as a sign that it is due to PCR duplication during library construction. In many analysis work flows these presumptive PCR duplicates are removed.