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