Dear Galaxy expert:
I have recently been using Galaxy and have been thrilled with its utility and ease. Thank you very much! I have one question - I am trying to fetch sequences (for C. elegans ce4 genome) for intervals in a tab delimited file that has been used successfully as an interval file for other types of Galaxy queries (attached). However, when I try to fish out the sequences associated with these intervals (for MEME analysis), I get empty returns, and the same warning (below). Where is it getting the 544 from? What do I need to do to make it read the file correctly? I tried file conversion, getting rid of the extra columns, and changing the chromosomes to I, II, III, etc (the canonical names in the worm field), and nothing seems to do the trick. Any suggestions would be helpful.
Thanks!
Valerie
Warning message:
empty format: fasta, database: ce4
Info: 2720 warnings, 1st is: Unable to fetch the sequence from '3525' to '544' for build 'ce4'. Skipped 2720 invalid lines, 1st is #1, "Chr1 3525 4069 281 21 3.25E-58"
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Valerie Reinke
Associate Professor
Dept Genetics
Yale University School of Medicine
203-785-5228
valerie.reinke@yale.edu