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  • Deciding how many reads map to a plasmid or to a genome

    Hi all,
    I have illumina genome reads for an E. coli a collaborator is studying. The prep used had a plasmid as well. I have two questions:

    1) For the reads that match both (e.g. lacI gene), how can I tell which came from the plasmid and which came from the genome?
    2) Should I normalize by dividing on the total reads per library or only the mapped reads in a library?

    Thanks in advance...
    Last edited by fznajar; 01-09-2019, 01:44 PM.

  • #2
    #1 = Unless there is/are SNP's which are captured by that particular read you would not be able to tell where the read came from. I assume the sequence of the gene is otherwise identical?

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    • #3
      You are correct GenoMax. They are identical. Appreciate it.
      Best

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      • #4
        If you'are using "bwa sampe" for aligning, the documentation says:

        Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly.
        I don't know if it is the case with "bwa mem" or with "bwa aln".

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