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Posts by Sergej.Nowoshilow
Comment: C: Automatic BAM indexing
... Yes, I have a set of custom tools and also adjusted some of the tools from the standard ToolShed. However, I have a feeling that many tools may be just fine if the .csi file is renamed to .bai. Those tools rely on HTS library and, therefore, this naming must be completely transparent for them as the ...
... Dear community, is there a way to modify the default way Galaxy creates the index *.BAI files? We work with a large salamander genome, therefore, quite some coordinates in the BAM files are beyond 2^30. Therefore, the index files have to be created using either biobambam2:bamSort or samtools index ...
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