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  • Pair-end bowtie questions

    Hello everyone!!
    I'm new in the work with sequencing, more specific Chip-seq data set. I have pair-end data and mapped it with bowtie2. I have read the SAM format specifications but don't understand column 7:

    "RNEXT: Reference sequence name of the primary alignment of the NEXT read in the template"

    Someone can explain me whats mean this? What means that the column possesses "=" or "*"?

    Greetings!!

  • #2
    * means the other read did not align. = means both are on the same reference sequence. Generally that's not an important field since it's just repeating information you can get by looking at the other read.

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