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Old 09-16-2014, 10:35 PM   #1
ramujana
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Default Minimum coverage info on Miseq

Hi,
does anyone can suggest how to extract MINIMUM coverage information of particular ROI after MiSeq run? (after standard fastq aligment to reference genome+manifest file and generating bam files)
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Old 09-17-2014, 11:29 AM   #2
westerman
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It depends on how longer your ROI (region of interest) is. If not too long you should be able to do multiple '-c' (count) via samtools one base at a time and then choose the smallest count. I haven't tried this and it would take a bit of shell scripting but it should be feasible as a one-off solution.
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Old 09-18-2014, 01:10 AM   #3
WhatsOEver
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"samtools depth" gives you the per base coverage and has a "-r" parameter with which you can define your ROI.
Alternatively, genomecov from bedtools works quite nicely for such questions (http://bedtools.readthedocs.org/en/l...genomecov.html)
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Old 09-18-2014, 07:21 AM   #4
westerman
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'WhatsOEver' has the much better solution. I knew that samtools could do the work -- it is a rather powerful program -- but how to do it was escaping me in my work-induced haste of reading SeqAnswers.
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