![]() |
|
![]() |
||||
Thread | Thread Starter | Forum | Replies | Last Post |
soapsnp segmentation fault - help! | jtjli | Bioinformatics | 6 | 02-29-2016 08:54 AM |
About SOAP and SOAPsnp | evonne16 | Bioinformatics | 7 | 04-20-2012 09:17 AM |
Getting Started with SOAPsnp | taylorm | Bioinformatics | 0 | 03-03-2011 10:51 AM |
SOAPsnp sort script | jgibbons1 | Bioinformatics | 4 | 06-09-2010 06:35 AM |
soapsnp error | Anna Esteve | Bioinformatics | 0 | 05-26-2010 07:11 AM |
![]() |
|
Thread Tools |
![]() |
#1 |
Junior Member
Location: Utah Join Date: Sep 2010
Posts: 2
|
![]()
I'm using SOAPsnp to identify SNP. Is there any visualization for SOAPsnp pileup?
Thanks, guys. |
![]() |
![]() |
![]() |
#2 |
Member
Location: Netherlands Join Date: Sep 2009
Posts: 43
|
![]()
What exactly do you want to visualize? If think you want to see the mapped reads and where they differ from reference (known/possible SNPs) as stacked output (so all complete reads!)... If so you should use mapping output to visualize that. For example SAM/BAM format in IGV, you will see all mapped reads stacked on top of the reference sequence. See links:
For SOAP I see there is a soap2sam converter (perl script): http://soap.genomics.org.cn/ In IGV you can load and view SAM/BAM: http://www.broadinstitute.org/igv/ Or try some other NGS viewer, for a software comparison: http://lh3lh3.users.sourceforge.net/NGSalnview.shtml |
![]() |
![]() |
![]() |
#3 |
Junior Member
Location: Utah Join Date: Sep 2010
Posts: 2
|
![]()
Thanks man!
|
![]() |
![]() |
![]() |
Thread Tools | |
|
|