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(a)bx.psu.edu, galaxy-bugs(a)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
>> _______________________________________________
>> galaxy-user mailing list
>> galaxy-user(a)lists.bx.psu.edu
>>
http://lists.bx.psu.edu/listinfo/galaxy-user
>>
>
> Guruprasad Ananda
> Graduate Student
> Bioinformatics and Genomics
> The Pennsylvania State University
>
>
>
>
>
Guruprasad Ananda
Graduate Student
Bioinformatics and Genomics
The Pennsylvania State University