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I am using STAR in a variety of different projects and it helped me a lot in many cases.
Recently, I started using STAR in a spatial transcriptomics protocol and I found really useful the add of the GN tag (corresponding to the Gene the read overlaps, if one and only one gene is overlapped) which is currently implemented in the STARsolo protocol.
However, since in this case I am only using the output bam file, it would save a lot of computation time and RAM usage to have the GN tag implemented in the plain STAR alignment. This is particularly true with spatial transcriptomics as the barcodes are way more than in scRNA-seq and STARsolo uses a lot of resources to keep track of barcodes while running, but the gene counts matrix in my case is not useful as mapped reads are then assigned to spatial coordinates by a different algorithm.
I believe that, apart from my case, in many other protocols having the GN tag in the output bam file would be really useful.
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I am using STAR in a variety of different projects and it helped me a lot in many cases.
Recently, I started using STAR in a spatial transcriptomics protocol and I found really useful the add of the GN tag (corresponding to the Gene the read overlaps, if one and only one gene is overlapped) which is currently implemented in the STARsolo protocol.
However, since in this case I am only using the output bam file, it would save a lot of computation time and RAM usage to have the GN tag implemented in the plain STAR alignment. This is particularly true with spatial transcriptomics as the barcodes are way more than in scRNA-seq and STARsolo uses a lot of resources to keep track of barcodes while running, but the gene counts matrix in my case is not useful as mapped reads are then assigned to spatial coordinates by a different algorithm.
I believe that, apart from my case, in many other protocols having the GN tag in the output bam file would be really useful.
Best,
Valerio
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