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  • BAM-Readcounts or R

    Hello, I am trying to get readcounts of coordinates of a gene I found on ucsc genome browser on some bam files I have. Is there some sort of protocol on how to use either bam-readcounts or "R" to do this quick analysis. I am new to linux and bioinformatics in general.

  • #2
    See this thread (an oldie) but should give you what you need: http://sourceforge.net/p/samtools/ma...sage/27419954/

    If you want the bare minimum steps (replace chr1:1234-2345 with actual coordinates of your gene, you may have to make sure that chromosome name matches what is in your bam e.g. chr1 vs 1).

    Code:
    $ samtools index input.bam
    $ samtools view input.bam chr1:1234-2345 | wc -l

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    • #3
      I haven't tried the other suggested methods, but bedtools multicov is extremely fast and simple to use.



      bedtools multicov \
      -bams bamFile.bam \
      -bed region.bed
      Last edited by blancha; 11-24-2015, 09:40 AM.

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