Question: Get Only Repeatmasked Exons
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Managadze, David (NIH/NLM/NCBI) [F] • 10 wrote:
Dear Galaxy expert(s),
I have .BED file of regions from mouse. I guess many of them can span
whole genes i.e. many exons; might even span over the gene flanks.
I need to get the REPEATMASKED sequences of only the annotated exons
of these regions.
I see that If I use the tool "Fetch Sequences->Extract Genomic DNA" on
these regions, it returns sequences with mixed small and capital
letters.
Question I: what are the small letters and what are the capitals here?
Are these already masked, exons/introns or what?
(I downloaded some of these sequences and repeatmasked myself. My
pasked sequences overlap with some of "yours" written in small
letters.)
Question II: Is the strand "honored" by these tool?
I guess I remember from my old experience that there was an issue
although I can not recall what exactly.
Thank you in advance,
David
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modified 7.1 years ago
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Anton Nekrutenko ♦ 1.7k
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7.1 years ago by
Managadze, David (NIH/NLM/NCBI) [F] • 10
