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  • how to summarize information for a gene from bam file

    I have very basic question about bam files, it may be very obvious but kind of stacked.

    I would like to see how many LINE,SINE etc are around the genes (which of my genes are enriched with repeats of LINE/SINE etc. elements).

    For this, I have aligned data in bam format and the repeats in bed format.

    As far as i know BAM files contains aligned data for each read from fastq file. How can i summarise information for each gene from a bam file? so that i can overlap these genes with the repeats and check for an enrichment?

  • #2
    You can use bedtools for this purpose. An example would be the multicov option: http://bedtools.readthedocs.org/en/l.../multicov.html

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    • #3
      Originally posted by roll View Post
      I have very basic question about bam files, it may be very obvious but kind of stacked.

      I would like to see how many LINE,SINE etc are around the genes (which of my genes are enriched with repeats of LINE/SINE etc. elements).

      For this, I have aligned data in bam format and the repeats in bed format.

      As far as i know BAM files contains aligned data for each read from fastq file. How can i summarise information for each gene from a bam file? so that i can overlap these genes with the repeats and check for an enrichment?
      The featureCounts program may help - http://bioinf.wehi.edu.au/featureCounts/

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      • #4
        Originally posted by GenoMax View Post
        You can use bedtools for this purpose. An example would be the multicov option: http://bedtools.readthedocs.org/en/l.../multicov.html
        Thanks, i was looking at this feature. It is fast but i also want to know the repeat elements that are within certain threshold, 500bp for example in the forward strand.
        This seems to be possible with bedtools windows option (-l -r) but not sure if it works with multicov. At least there is no option in the help menu.

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