This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Megan 5 - How To Extract All Read Assignments To A Dsv

I would like to export assignment of each read to taxon_id (from NCBI tree). When I go to File -> Export -> DSV Format, and then choose format "read-name, taxon-id" I have to select some node otherwise 0 lines are written to file. Also when I collapse subtree, all assignments of a subtree are mapped to the parent node, e.g. Bacteria and real assignments are ignored.

So how do i get real assignments and for all reads? Do I have to uncollapse whole tree and then select all nodes?

• 3,927 views • link
written by matija.sosic • matija.sosic

ok, but isn't it the easiest to actually try what you suggest and see if it that does it?

• 157 views • link
written by Istvan Albert Istvan Albert

1 answer

Select Tree -> uncollapse all and then press ctrl + a to select all nodes. Having all nodes selected, File -> Export -> DSV Format will export all of them.

• 0 views • link
written by matija.sosic • matija.sosic

Log in to answer this question.

More posts like this