N50 and N90 contig size refer to? - Page 2

edge · 10-08-2009, 12:13 AM

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

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

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

BENM · 10-08-2009, 03:32 AM

Quote:

Originally Posted by edge

Hi BENM,
If I got a long list of contents:
scaff_123 20
scaff_223 60
scaff_122 1000
scaff_125 15
scaff_23 30
scaff_13 26
scaff_230 50
scaff_153 500
scaff_173 200

Based on the column two,
Do you have any idea how to calculate the N50 and N90 from this long list of contents?
I need to do descending order of this long list of contents before I calculate the N50 and N90,right?
Thanks again for your help

hi edge,

I have written a PERL script for stat. length and gc content of FASTA/FASTQ file, hope it ould help you.

edge · 10-08-2009, 05:51 PM

Hi BENM,

Thanks a lot for your script.
I just run it d.
It worked excellent and fast.
I and sklages facing the same problem of the output result of MIRA.
Still finding the solution now.
Thanks again for your explanation and script

BENM · 10-08-2009, 06:58 PM

Quote:

Originally Posted by edge

Hi BENM,

Thanks a lot for your script.
I just run it d.
It worked excellent and fast.
I and sklages facing the same problem of the output result of MIRA.
Still finding the solution now.
Thanks again for your explanation and script

hi Edge,

The "calengc.pl" has a bug in stat. gc content, it has been corrected.

edge · 10-08-2009, 07:04 PM

Hi BENM,
Thanks for your remind. Can I know what you mean by "The "calengc.pl" has a bug in stat. gc content, it has been corrected. "?
You are a perl programmer expert?
Seem like the perl script you write can deal with data quite fast

BENM · 10-08-2009, 07:22 PM

Hi Edge,

I don't think I am PERL programmer expert, just a junior learner.
It is the same as python or C/C++, or other program language, I think the most important is algorithm or thinking idea. Just PERL can be written easily.
I have another bug in length stat. Sorry for my slack.

edge · 10-08-2009, 07:25 PM

I very appreciate for your script.
I also prefer perl too.
In between, I feel awk and sed sometimes also quite useful as well.
Can I know what is the bug or error that you have been written at gc content and length stat?

milo0615 · 07-13-2015, 03:13 PM

Hi BENM,

Did you post the corrected 'calengc.pl' script?

Quote:

Originally Posted by BENM

hi Edge,

The "calengc.pl" has a bug in stat. gc content, it has been corrected.

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10-08-2009, 05:51 PM	#23
edge Senior Member Location: China Join Date: Sep 2009 Posts: 199	Hi BENM, Thanks a lot for your script. I just run it d. It worked excellent and fast. I and sklages facing the same problem of the output result of MIRA. Still finding the solution now. Thanks again for your explanation and script

10-08-2009, 07:04 PM	#25
edge Senior Member Location: China Join Date: Sep 2009 Posts: 199	Hi BENM, Thanks for your remind. Can I know what you mean by "The "calengc.pl" has a bug in stat. gc content, it has been corrected. "? You are a perl programmer expert? Seem like the perl script you write can deal with data quite fast

10-08-2009, 07:22 PM	#26
BENM Member Location: PRC Join Date: May 2009 Posts: 33	Hi Edge, I don't think I am PERL programmer expert, just a junior learner. It is the same as python or C/C++, or other program language, I think the most important is algorithm or thinking idea. Just PERL can be written easily. I have another bug in length stat. Sorry for my slack.

10-08-2009, 07:25 PM	#27
edge Senior Member Location: China Join Date: Sep 2009 Posts: 199	I very appreciate for your script. I also prefer perl too. In between, I feel awk and sed sometimes also quite useful as well. Can I know what is the bug or error that you have been written at gc content and length stat?