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
David:
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.)
In case of mouse the sequences are extracted from softmasked genomic builds retrieved from UCSC. So, small lettres = repeats, capital letters = no repeats.
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.
Yes, if the strand is explicitly specified. If it is not specified it is assumed to be +. Thanks for using Galaxy. anton
Thank you in advance,
David
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
-
Anton Nekrutenko -
Managadze, David (NIH/NLM/NCBI) [F]