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Old 11-13-2011, 06:37 AM   #1
akvarel
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Default all depths

Hello!
I was using Newbler Assembler and Mapper and I got results like alignment depth, total depth, unique depth.

What are the differences between them and what do they mean?

I know that alignment depth is how many times each secuenced base is covered.
What is with others?


Thanks.
Katja
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Old 11-14-2011, 01:21 AM   #2
flxlex
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From the manual:
Unique Depth – the number of non-duplicate reads that align at that position in the alignment
Align Depth – the number of reads (including duplicates) that align at that position in the alignment
This regarding the 454AlignmentInfo.tsv file...
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Old 11-14-2011, 03:24 AM   #3
akvarel
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Thank you but you forgot to write as well what total depth ist.
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Old 11-15-2011, 02:04 AM   #4
flxlex
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Where is this 'Total Depth' reported?
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