SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
megan5:Parse error: java.util.NoSuchElementException vinumanikandan Bioinformatics 0 02-25-2015 10:23 PM
NCBI eutils, perl, a small parsing problem rhinoceros Bioinformatics 2 08-04-2013 11:01 AM
bioperl blast parsing problem Mark Bioinformatics 9 04-27-2013 04:22 PM
parsing bam taha.hojati Bioinformatics 2 06-19-2012 03:52 PM
Parsing COSMIC Lee Sam Bioinformatics 0 06-28-2010 07:11 AM

Reply
 
Thread Tools
Old 07-29-2015, 12:29 AM   #1
Letia
Junior Member
 
Location: Göttingen

Join Date: Jul 2013
Posts: 1
Default MEGAN5: parsing problem?

I have an assembled transcriptome that I blasted against the nr_db from NCBI. I want to use MEGAN to get some taxonomic information on the reads. I imported my blast xml files into MEGAN5 and all seemed to work fine. When I click a node to inspect which hits are associated with a given taxon I encounter a problem. The majority of the hits are listed correctly with the query id header but some do not have a header and the hole sequence or parts of a sequence is displayed. This results in incomplete sequences when I want to extract subsets of reads. This is how it looks like: Screen Shot 2015-07-27 at 12.14.39.png

I have no clue what is happening there and how to fix it. Anyone encountered a similar problem?

Could there be a problem with the blast xml input files? Or is it a parsing problem? Any idea how to fix this?

Any help is apreaciated!
Letia is offline   Reply With Quote
Old 09-04-2015, 07:05 AM   #2
hoytpr
Member
 
Location: Stillwater

Join Date: Dec 2009
Posts: 62
Default

Hello Letia,
I am having the same problem and have emailed Daniel Huson about it. I worry it is something I have done wrong, but hopefully Daniel can recognize it and tell me what to do correctly.

Peter
hoytpr 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 06:24 AM.


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