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Old 03-05-2014, 01:13 PM   #1
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

/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
Location: USA

Join Date: Mar 2010
Posts: 50

Try Tigra-SV
m_two is offline   Reply With Quote
Old 03-06-2014, 06:27 AM   #3
Carrot Scientist
Location: Madison WI USA

Join Date: Nov 2009
Posts: 42

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:

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
/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

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