Hello,

I am trying to extract sequences from a FASTA file containing genomic 
information. The coordinates are in a tab-delimited format, which is recognized 
as BED format by Galaxy (meaning that the 6th column is correctly interpreted 
as 6. Strand).

However, upon running "Fetch sequences" , Extract Genomic DNA only the +-strand 
information is included in the output FASTA file and I receive the following 
ERROR message:

1,431 sequences
format: fasta, database: ?
Info: 1476 warnings, 1st is: Invalid interval, start '1616' > end '1177'. 
Skipped 1476 invalid lines, 1st is #2, "scaffold00001   1616    1177    Fom -   
1"

Is this a bug? How can I can adjust my input data files to get the --strand 
sequences as well?

I have seen a similar problem in an earlier posting and there it was suggested 
to manually adjust the strand information column 5, but this did not work for 
me neither.

Many thanks for your all help!!!!!


Sarah
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to