SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
De novo assembly using Velvet: any idea why such small Kmers with long reads? Genomics101 Bioinformatics 17 02-21-2014 05:12 PM
Inquiry: minimum length of reads for referece-based assembly or de novo assembly sunfuhui Bioinformatics 1 10-04-2013 09:28 AM
Finding SMALL peptides in de novo assembly gege_55 Bioinformatics 3 03-07-2013 01:06 AM
bowtie on small region yimmieg Bioinformatics 2 01-17-2011 01:46 PM

Reply
 
Thread Tools
Old 03-05-2014, 01:13 PM   #1
nimrod337
Member
 
Location: Wisconsin

Join Date: Jun 2013
Posts: 22
Default De novo assembly of a small region after using PINDEL?

Hello again,
I have just recently got the program PINDEL to work on my reads, and it identified a large deletion (9kb) in my region of interest (gene family, roughly 40kb). What I would really love, is to take all the reads from PINDEL, and my original alignment from that particular area, and re-align them without the reference, to see if it can make sense of the region. Has anyone had any luck doing such a thing? If so, can you point me in the right direction?
Thanks so much
A

/I've also already designed primers to test if this deletion is legit, so that's obviously a first step.
nimrod337 is offline   Reply With Quote
Old 03-05-2014, 02:19 PM   #2
m_two
Member
 
Location: USA

Join Date: Mar 2010
Posts: 50
Default

Try Tigra-SV

http://gmt.genome.wustl.edu/tigra-sv/0.1/index.html
http://genome.cshlp.org/content/24/2/310
m_two is offline   Reply With Quote
Old 03-06-2014, 06:27 AM   #3
dsenalik
Carrot Scientist
 
Location: Madison WI USA

Join Date: Nov 2009
Posts: 42
Default

Tigra looks interesting, but from what I can tell that version is no longer being developed, and the original author now has version 0.3.9 here:

http://bioinformatics.mdanderson.org/main/TIGRA

Also, neither of these will compile with samtools 0.1.19, but 0.1.18 works.
For the benefit of Google searchers, the error message with 0.1.19 is
Quote:
/usr/lib/samtools/libbam.a(bgzf.o): In function `bgzf_mt':
.../samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'
/usr/lib/samtools/libbam.a(bgzf.o): In function `mt_destroy':
.../samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'
dsenalik 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 01:47 PM.


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