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Old 10-08-2009, 12:13 AM   #21
edge
Senior Member
 
Location: China

Join Date: Sep 2009
Posts: 199
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Yup...
Seem like we facing the same problem
Maybe need ask and sharing the experience from other users
I will share with you if I find out the solution to match all the figure with the
*_info_contigstats.txt

Quote:
Originally Posted by sklages View Post
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
Quote:
Originally Posted by sklages View Post
Well, you are right. I just checked for this as well. N50 and "largest contig" are "correct" (in a sense how I calculated it), all other numbers differ slightly from what I was counting ...

No idea why ..
Sven
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