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Old 05-22-2009, 12:29 PM   #1
gaster
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Default Summary Statistics in Newbler?

The Mapper output comes with handy xls file with a lot of great statistics in it. The Newbler output doesn't seem to have anything like this? I am particularly looking for statistics about the coverage in the contigs (avg, min, max, etc.)

Anyone know where this info is or a good program to use to find it?
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Old 05-23-2009, 12:49 AM   #2
sklages
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Hi,

you might want to have a look at 454NewblerMetrics.txt (or csv) for assembly statistics and 454ReadStatus.txt to see what happened to your reads ...

A detailed contig description (for parsing) gives you 454AlignmentInfo.tsv .

hth,
Sven
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Old 05-25-2009, 11:34 PM   #3
flxlex
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And/or have newbler produce the 454ContigGraph.txt file which gives you average coverage per contig (not min/max). This can be done by setting the -g flag (note: this sets the minimum contig length to report from 100 bp to 1 bp...).
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Old 05-28-2009, 07:17 AM   #4
gaster
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Thanks for your reply, Flxlex. Couple questions: How do you set the g-flag? Is there no way to get min/max coverage?

Thanks.
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Old 05-28-2009, 07:21 AM   #5
gaster
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Thanks, Sklages. The metrics files don't seem to have info about coverage, right?

The 454AlignmentInfo.tsz files only gives me partial info on one contig. Is that right? It can't be. Any ideas?

Thanks so much.
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Old 05-28-2009, 09:33 AM   #6
sklages
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The 454NewblerMetrics.txt reports only common stats about the assembly.

Well, and the tsv file covers all contigs:

Code:
$ fgrep -c \>contig 454AlignmentInfo.tsv
430
$ fgrep -c \> 454AllContigs.fna
430
cheers,
Sven
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Old 05-28-2009, 12:14 PM   #7
kmcarr
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gaster,

Are you using the Roche GUI (gsAssembler) to view the 454AlignmentInfo.tsv? If so this viewer truncates the display at 50,000 lines. The file is located in the assembly subdirectory of your main project directory. You can view the entire file with a standard text editor. (Careful, if your assembly is large this file will get huge.) You will need to process the file using some sort of script to extract and calculate the coverage information you asked about (ave, min, max, etc.).
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