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  • Obtain coordinates of insert (e.g. bed file) from aligned paired-end reads (sam file)

    Hi,

    I am just trying to obtain start and end coordinates of the insert (something like a bed file) from my alignment file (.sam) of paired-end reads (that is to reconstruct the fragment information in one lign from the information of both aligned mates stored in two ligns in the sam file)
    I aligned my paired-end reads with bowtie2 and only retained paired reads aligning only one time.
    I am looking for a tool doing this but was unable to found something that already exists.

    Does anyone have an idea for doing this?

    Thanks for your advices!

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