SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
velvet- stats.txt file vani s kulkarni Bioinformatics 4 12-10-2019 08:42 PM
velvet's output: Roadmaps shuang Bioinformatics 1 08-18-2011 01:43 PM
Stats from SOAPdenovo output files JolienC De novo discovery 2 11-24-2010 03:28 AM
Velvet -output format rbm_rk De novo discovery 1 07-28-2010 09:36 AM
splicing stats from Tophat's SAM output darked89 Bioinformatics 0 04-29-2010 11:51 AM

Reply
 
Thread Tools
Old 01-19-2010, 12:41 PM   #1
ytmnd85
Member
 
Location: Nebraska

Join Date: Apr 2009
Posts: 10
Default Velvet - stats output - min_contig_length

I am attempting to use Velvet to analyze some data from our lab. During a practice run, I noticed that the output from velvet had some odd contigs (length 1, coverage 300,000), so I decided to place some parameters on it. I set the minimum coverage to 10, and the minimum contig length to 10. When I checked the new output, the minimum coverage had been implemented, but it didn't appear that the minimum contig length had. Looking at the stats file, I still had contigs of length 1. However, upon looking at the contigs.fa file, I found that my contig length had been implemented.

Does anyone know why my contig file is correct, but my stats file does not reflect my contig-length restriction?
ytmnd85 is offline   Reply With Quote
Old 01-19-2010, 01:38 PM   #2
Zigster
(Jeremy Leipzig)
 
Location: Philadelphia, PA

Join Date: May 2009
Posts: 116
Default

Quote:
Does anyone know why my contig file is correct, but my stats file does not reflect my contig-length restriction?
yeah that parameter only affects the contigs.fa file (as you have already discovered)

min_contig_length is just a dumb cutoff included for convenience - a two-line perl script could accomplish the same thing

cov_cutoff is a real parameter that can actually change the assembly in unexpected ways

and also note that length in the stats.txt file is in kmers, not bp
__________________
--
Jeremy Leipzig
Bioinformatics Programmer
--
My blog
Twitter
Zigster is offline   Reply With Quote
Old 01-19-2010, 02:14 PM   #3
ytmnd85
Member
 
Location: Nebraska

Join Date: Apr 2009
Posts: 10
Default

Thank you,
That makes sense now. It just had me perplexed when I was trying to interpret my results and I was seeing contradicting files.
ytmnd85 is offline   Reply With Quote
Old 01-24-2014, 03:34 AM   #4
mmmm
Senior Member
 
Location: UK

Join Date: Jul 2013
Posts: 131
Default kmer to nucleotide

Quote:
Originally Posted by Zigster View Post
yeah that parameter only affects the contigs.fa file (as you have already discovered)

min_contig_length is just a dumb cutoff included for convenience - a two-line perl script could accomplish the same thing

cov_cutoff is a real parameter that can actually change the assembly in unexpected ways

and also note that length in the stats.txt file is in kmers, not bp
in stats.txt (velvet output) how to convert node length to the actual nucleotide length, for example, if the node length is 1what would be the nucleotide length?
mmmm is offline   Reply With Quote
Old 01-24-2014, 04:33 AM   #5
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 667
Default

see the equation for calculating kmer coverage from nucleotide coverage in the velvet manual.

http://www.ebi.ac.uk/~zerbino/velvet/


"The relation between k-mer coverage Ck and standard (nucleotide-wise) coverage C is Ck = C (L−k +1)/L where
k is your hash length, and L you read length."


Node length = Contig length in nucleotides minus k-mer length + 1.

Last edited by mastal; 01-24-2014 at 04:53 AM.
mastal is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:13 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO