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  • Is there a conventional way to report sequencing stats for paired-end experiments?

    Hi all,

    I was wondering if there is a preferred way to report the read statistics (such as the number of uniquely aligned reads) specifically for paired-end experiments? We were asked to provide a Supplementary table with read counts for all of our ChIP-seq and RNA-seq experiments for our paper. All our experiments are paired-end sequencing, however, I failed to find a consistent way the sequencing stats are reported for this type of experiments in the papers: some people report number of reads, some - read pairs. Does it really matter? If someone could point me in the direction of a comprehensive guide with good practices of how this information should be reported in general, I would really appreciate it!

    P.S. I am also unclear about whether the number of reads before alignment has to be reported as well or only the number of uniquely aligned read used for the analysis is important.

    Thank you very much in advance for your help!

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