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2019-02-27 18:14:04 -0600 | asked a question | gautil coverage failing to identify genome assembly I am trying to use gautil coverage on my Mac to produce the coverage graphs (and zoomed out pile-up) prior to loading .bam files into GenomeBrowse, as if I have a lot of .bam files and if they are only processed one by one in GenomeBrowse GUI, it takes a very long time. I am running the following command from within the GenomeBrowse 'Tools' folder where gautil is located: And the output I receive is as follows: It seems to me that gautil is unable to identify which genome assembly my alignments are to in my .bam. When I drag and drop the same .bam file into GenomeBrowse it is able to do the computation fine, so I am not sure what the problem is. I have tried using different .bam files and also I have tried specifying the .tsf reference sequence file path directly instead of specifying the path to the folder containing it, but these didn't work. A colleague of mine seems to be doing the same thing as I am doing on Windows but having it work, so I am wondering whether this is a Mac-specific issue, or whether I am making some mistake in replicating his method. |