Question: Question About Galaxy
gravatar for Jennifer Hillman Jackson
6.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hi Qianli, It looks as if you are using the Extract DNA tool? GTF/GFF files have coordinates with a 1-based start position - and this was your input, but the output from this tool produces coordinates with a BED-style 0-based start position. The genome index files used by the tool are in .2bit format and the source is encoded into the full name. The sequence content of the reference genome is not altered by the tool. Perhaps the interpretation of the coordinates is the source of the difference or you are sourcing a different version? If you have a question about where we sourced a genome, please let us know. To see a quick description of both BED and GFF format together in the UI, click into the tool "Convert Formats -> GFF-to-BED converter". For more in-depth descriptions, please see our wiki: Next time, please send questions directly to our mailing list, with the "to" address as Best, Jen Galaxy team -- Jennifer Jackson
gff • 667 views
ADD COMMENTlink written 6.5 years ago by Jennifer Hillman Jackson25k
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