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Hello! Can anybody let me know, how can I get coverage data of a single gene from BAM file. Thanks.
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Where contig is the name of the chromosome, 12 is the start position of your gene and 1000 is the end position.Code:samtools depth -r contig:12-1000 single.bam
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Use BedTools -- coverageBed should be the program you want.
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Actually TiborNagy's method is easier for a single gene. Give that a try first.
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