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Old 03-15-2014, 10:08 PM   #1
Junior Member
Location: Pakistan

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Default SOLiD sequencing

Hello! Can anybody let me know, how can I get coverage data of a single gene from BAM file. Thanks.
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Old 03-17-2014, 05:47 AM   #2
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Location: Budapest

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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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Old 03-17-2014, 06:01 AM   #3
Rick Westerman
Location: Purdue University, Indiana, USA

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Use BedTools -- coverageBed should be the program you want.

Actually TiborNagy's method is easier for a single gene. Give that a try first.
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