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  • question regarding MeDIP package

    I have three replicates of control and treatment for MeDip-Seq data. I am also looking into whole genome.

    I have used bowtie2 before to align the reads for each of the fastq files.

    1. generate fasta files for interested regions
    2. use bowtie2-build to create index files
    3. then use bowtie2 for alignment and generate sam files and from there generate bam files.

    In the MeDIPS package they have two different bam files (MEDIPS Tutorial - Lukas Chavez)

    (1) bam files that are bowtie mapping results of MeDIP-seq data derived from the three replicates of human embroynic stem cells and replicates of differentiated hESCs.

    (2) For each condition there is one bam file containing the mapping result of corresponding Input-Seq data.


    So I want to know how each bam files can be generated separately for (1) and(2). I thought that the mapping was already done with with the bowtie and then generate the bam files. then how can I get bam files for option (2).

    Thanks in advance.

  • #2
    Looks like option(2) is not necessary and its optional.

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