[galaxy-dev] tabular to bed

[Matthias Bernt]

Dear galaxy-devs,






But, in particular using awk seems to be "end user incompatible" :)

What would be the best idea: Provide a workflow or a tool doing the job?



Anyway there has been a problem:


1.Chrom 2       3.Name  4       5       6       7       8.Start 9.End   
10.Strand       11      12      13      14      15      16      17      18





Thanks for all the help.

Best,
Matthias

--

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Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de

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Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------

What would be the galaxy way to convert tabular data (e.g. the tabular output of BLAST or infernal) into bed or alignments? For bed it seems like that cutting the columns and using awk to adapt the positions to the bed definitions and switch coordinates for the reverse strand matches would do the job. Initially I had hoped that I can simply change the data type to bed and assign the columns in the attributes tab (but I forgot about the coordinate adjustments). Then the preview in the history shows that the columns are assigned (except for the score column). It looks like this: But in "Show Data" the columns are still taken as is, e.g. 2nd column is start ... When I try to use the File in BedTools Merge it fails with the message that it is not a bed file. Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus

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