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  UGENE Forum › General Category › Feature Requests › How to export base-by-base alignment coverage data?
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How to export base-by-base alignment coverage data? (Read 13379 times)
Dec 15th, 2012 at 2:57am

brianm   Offline
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I've aligned sequences to a reference and would like to output a table that shows the depth of coverage at each position using the reference sequence base numbering.
 
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Reply #1 - Dec 17th, 2012 at 5:43pm

Yuriy Vaskin   Offline
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There is no way to export such information. Only visualization is available yet. But we already planned to implement it (https://ugene.unipro.ru/tracker/browse/UGENE-453)
 
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Reply #2 - Apr 2nd, 2014 at 6:39am

Adam   Offline
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Is there a work around for this? I'd really like a list of reference positions in one column, and coverage depth in a second column.
 
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Reply #3 - May 9th, 2014 at 3:19pm

Yuriy Vaskin   Offline
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We integrated bedtools genomeCov which has a number of options to show the coverage. It will be available in the next releases
 
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