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Old 10-08-2009, 12:02 AM   #19
edge
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Location: China

Join Date: Sep 2009
Posts: 199
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Hi sklages,

You are right d.
I think I do calculate N50 using *_info_contigstats.txt (which gives the same as results as if I use the contigs.fasta file).
At the above sentence, we should use *_out.unpadded.fasta instead of contigs.fasta file to calculate N50,right?
I try using contigs.fasta file to calculate the N50 but it can't match with the
*_info_contigstats.txt. However, *_out.unpadded.fasta can do it
It seem like contigs.fasta file same with the *_out.padded.fasta file, both just the header a bit different, right?
Besides that, refer to the *_info_assembly.txt at Section "All Contigs". I try to use the *_info_contigstats.txt/contigs.fasta file/*_out.unpadded.fasta to find out the "Total consensus","Number of contigs",etc at Section "All Contigs".
Unfortunately, it can't match with the figure at Section "All Contigs".
Do you have any idea about this problem facing?
It seem like all the figure that I get from the file (*_info_contigstats.txt/contigs.fasta file/*_out.unpadded.fasta) is lesser than the figure at Section "All Contigs"


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).
cheers,
Sven
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