SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Fusion Hunter for Finding Fusion genes alvarani Bioinformatics 3 07-20-2015 08:21 AM
Fusion-gene finding (in search for THE read-length) ljq Bioinformatics 1 05-12-2014 01:37 AM
Finding common genomic regions... milesgr Bioinformatics 0 03-27-2013 05:54 AM
Finding *new* regions of DNA in genome assemblies green tree De novo discovery 5 02-20-2012 02:19 PM
Finding regions of enriched sequence tags droog_22 Bioinformatics 0 01-09-2012 07:09 AM

Reply
 
Thread Tools
Old 07-06-2018, 10:21 AM   #1
rahilsethi
Member
 
Location: Pittsburgh, PA

Join Date: May 2010
Posts: 22
Default ViralFusionSeq not finding human-virus fusion regions

I ran ViralFusionSeq, first on test dataset, given with the software package. I took one the contig assembly sequence generated by tool in the final contig output file. The contig sequence showed BLAST hits with human and hbv virus. I repeated the same procedure with HIV and human, on sample where I manually found clipped sequences that are shared between the two genomes. I then BLAST aligned contig sequences to both human and HIV virus. They only map to HIV. Why am I seeing this? The run was fine without any error reported. The data was DNASeq so I didn't provide any ORF, because I wanted to see all HIV-human integration regions, not only at specific ORF regions.

viral.fusion.pl --config vfs.conf --thread 8 sample_name sample_trim_1.fq sample_trim2.fq

Has anyone noticed such output?
Attached Files
File Type: txt vfs.conf.txt (3.3 KB, 0 views)
rahilsethi 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 08:33 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO