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Old 07-29-2015, 12:29 AM   #1
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
Location: Stillwater

Join Date: Dec 2009
Posts: 62

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.

hoytpr is offline   Reply With Quote

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