On Fri, Sep 17, 2010 at 7:08 PM, John McPherson
<John.McPherson@oicr.on.ca> wrote:
I think that you have extracted the “+” strand for your comparison. Below is the “-” strand from UCSC hg18
>hg18_dna range=chr10:123229360-123229525 5'pad=0 3'pad=0 strand=+ repeatMasking=lower
TTCATGTTTTAACACTGCCGTTTATGTGTGGATACTGAGGAAGGCATGGT
TCGTAAGGCATGGGGTCTGGAGAAAAAACAGAATCATCTCCTGAAGAACA
AGAACTTCTTGTGTCAGGGTAACTAGGTGAATACTGTTCGAGAGGTTGGC
TGAGGTCCAAGTATTC
>hg18_dna range=chr10:123229360-123229525 5'pad=0 3'pad=0 strand=- repeatMasking=lower
GAATACTTGGACCTCAGCCAACCTCTCGAACAGTATTCACCTAGTTACCC
TGACACAAGAAGTTCTTGTTCTTCAGGAGATGATTCTGTTTTTTCTCCAG
ACCCCATGCCTTACGAACCATGCCTTCCTCAGTATCCACACATAAACGGC
AGTGTTAAAACATGAA
On 10-09-16 11:28 PM, "gireesh bogu" <gireeshkbogu@gmail.com> wrote:
Dear Galaxy
I found a bug in extracting FATSA sequence tool in galaxy.
I extracted sequence of this location chr10 123229360 123229525 fgfr2 0 -
>hg18_chr10_123229360_123229525_-
GAATACTTGGACCTCAGCCAACCTCTCGAACAGTATTCACCTAGTTACCC
TGACACAAGAAGTTCTTGTTCTTCAGGAGATGATTCTGTTTTTTCTCCAG
ACCCCATGCCTTACGAACCATGCCTTCCTCAGTATCCACACATAAACGGC
AGTGTTAAAACATGA
And I checked back in UCSC browser by pasting the same location. The sequences are completely different (hg18).
Could you please help me in this issue
Thanx
Gireesh