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Old 10-07-2009, 11:28 PM   #18
sklages
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Location: Berlin, DE

Join Date: May 2008
Posts: 628
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Quote:
Originally Posted by edge View Post
Hi sklages,
Thanks for your suggestion.
I face some problems when try to find out the N50,N90,minimum contig size and maximum contig size,etc based on the *.contig file at "projectname_d_result".
The figure I find out can't match with the *_info_assembly.txt
Do you have any idea to calculate the N50,N90,minimum contig size and maximum contig size at *_info_assembly.txt ?
I do calculate N50 using *_info_contigstats.txt (which gives the same as results as if I use the contigs.fasta file).
This gives the same as the N50 calculated in *_info_assembly.txt (Section "All Contigs"!).

Btw, .. the padded fasta output contains the sequences with pads (if there are pads). The unpadded sequence has all pads been removed and is usually used for further analysis (but this depends on what you are doing).

cheers,
Sven
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