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Thread Tools |
04-15-2011, 01:56 AM
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#1 |
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Member
Location: France Join Date: Feb 2011
Posts: 11
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Samtools sort output smaller than input
Hello,
I have a problem with samtools sort : my output files are smaller than my input files when they should be identical since only the lines order is changed ! Does anyone know this problem and a solution ? thanks |
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04-15-2011, 03:06 AM
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#2 |
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Senior Member
Location: Cambridge, UK Join Date: Jul 2008
Posts: 146
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It is correct and is caused by higher compression ratios from zlib when data is sorted.
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04-15-2011, 09:10 AM
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#3 |
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Senior Member
Location: San Diego Join Date: May 2008
Posts: 912
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Right, this is normal. You can confirm that yourself by running flagstat on the unsorted and sorted file. They will have the same number of reads.
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04-15-2011, 02:12 PM
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#4 |
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Member
Location: France Join Date: Feb 2011
Posts: 11
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Indeed they have the same read number.
Many thanks for your help ! |
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