Hi Amit,

I was not able to reproduce the issue reported by you. I downloaded the BED file from the website pointed by you, and fetched sequences successfully. I'm sharing my history with you: http://main.g2.bx.psu.edu/u/guru/h/test-for-amit

Please make sure that you have the correct BED file, and correct metadata settings (chr,start,end columns and genome build).

Also, in future, can you please report your questions/issues to one of our mailing lists: galaxy-user@bx.psu.edu, galaxy-bugs@bx.psu.edu?

Thanks,
Guru.

On Mar 30, 2010, at 7:43 AM, pande wrote:

Hello GURU,
I am having problems with retrieving the FASTA sequences in the genomic interval that I took from
http://dir.nhlbi.nih.gov/Papers/lmi/epigenomes/hgtcell.aspx for the CTCF binding site.
The sequence file that I am getting is empty.

Please help.

warm regards,
Amit.


Guruprasad Ananda wrote:
Hello Amit,

The genomic sequences hosted on Galaxy are from UCSC and according to their convention repeats from RepeatMasker and Tandem Repeats Finder (with a period of 12 or less) are shown in lower case and non-repeating sequence is shown in upper case.

Hope this answers your question.
Thanks for using Galaxy,
Guru.


On Mar 11, 2010, at 5:02 AM, pande wrote:

 
Dear Galaxy,
                     I have the results for the sequence retrieval for Insulator regions in the human genome and I am having difficulty in comprehending the upper and lower case associated with my sequences.I know it for sure that they are regions which do not in any way overlap with exons or introns and  are that between any 2 genes.
I am attaching a small part of the sequence file for you to see and help me.


warm regards,
Amit.
   
hg19_chr14_100364027_100364047_+
     
AAGGCTTCTAATTTGGGTCT
   
hg19_chr14_100364319_100364339_+
     
TATTTTCCCAGCAGAGGATG
   
hg19_chr2_21174437_21174468_+
     
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
   
hg19_chr19_50965398_50965458_+
     
TGTCTCAAGGGATTTAGTCACTTAAAAAAtttttttaattgatttttgat
tttttttttt
   
hg19_chr19_50965141_50965201_+
     
ATCCTCTCTCCCCAGGAATCACCTTCAAACCGTTCGAGTATAAGGAGCAT
GACTTCCGGA
   
hg19_chr16_23597358_23597397_+
     
acccctcagactcccgagtagctgggattataggcgtgc
   
hg19_chr11_5269210_5269281_+
     
TCTTCCAAAACATCTGTTTCTGAGAAGTCCTGTCCTATAGAGGTCTTTCT
TCCCACCGGATTTCTCCTACA
   
hg19_chr11_5182745_5182816_+
     
ggaggaccgtaagggatataaaggttttactgaatactaagagcctgaaa
aactgcttggctgatttgact
   
hg19_chr11_1947003_1947086_+
     
CCAGGCCCCCTCACAGCCTTCTGCTATGAGACCCTTGAGGTGCACACAGG
CTGGGAGCAGATGGGAGGGCTGGGGTCCCATGC
   
hg19_chr11_1944457_1944540_+
     
GGGCCTCGTCTTTTCCCCGAAGTGTGGCCACATGGTCCTGAGGGGCCTGC
AGGTCAGGCTCTGGGTCCTGTCTCTCTGCTTCT
   
hg19_chr17_38531956_38532012_+
     
cctgggctcccacttcggtggcacttgaggagcccttcagcccaccgctg
cactgt
   
hg19_chr17_38531327_38531376_+
     
gatggtaacttcccggtggttaggttgttgccatggaaaggggcggtaa
   
hg19_chr3_10181494_10181542_+
     
taattctttcattttttatagagacaggacctcgctatgttgcccagg
   
hg19_chrX_23982287_23982341_+
     
ATTAGTGCATTCTTTTTCAGAAATTTTTTCTGTGCAGATATACAATCTGT
ATAC
   
hg19_chrX_23982417_23982470_+
     
TTAATAAACATGTCACTGCtgttgtgggtggggttgcccaggaaacagac
tct
   
hg19_chr11_2112020_2112170_+
     
CACCTTGCAGGGTCCCACCAAGACCACTGCAGCCTGGAATTTCCTGCTGA
CACTGGACGTAGGAGGCCTGGAGGGCCTGCAGGGGTCAGCCAGCGCCTCC
AGGACCCTCACTCAAACCTTGTCCCACGCCTTACCACCTTGCACCTGGTC
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Guruprasad Ananda
Graduate Student
Bioinformatics and Genomics
The Pennsylvania State University




 


Guruprasad Ananda
Graduate Student
Bioinformatics and Genomics
The Pennsylvania State University