Mike,
There actually is not a way to get the deleted base(s) from the SAM alone, since SAM displays only the read and not the reference.
Thanks, Kelly
On Wed Jun 8, at 4:58 PM, Mike Dufault wrote:
Hi All,
Does anyone know if there is a way to get the deleted base information that corresponds to the "Extract indels from SAM" output?
The output from this tool includes the bases for insertions or "-" for deletions. I want to get the actual bases instead of the "-".
I assume there is a way to use the SAM file to extract the information, but if someone already has a nifty way to do it, that would be great.
Thanks, Mike ___________________________________________________________ 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:
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