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  • SOLiD sequencing

    Hello! Can anybody let me know, how can I get coverage data of a single gene from BAM file. Thanks.

  • #2
    Code:
    samtools depth -r contig:12-1000 single.bam
    Where contig is the name of the chromosome, 12 is the start position of your gene and 1000 is the end position.

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    • #3
      Use BedTools -- coverageBed should be the program you want.

      [edit]
      Actually TiborNagy's method is easier for a single gene. Give that a try first.
      [end of edit]

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