Comments (2)
sztankatt
commented on September 4, 2024
This is ok, as merging happens after the unaligned_bc_tagged.bam step. Unaligned .bam files from different samples are merged, and then everything is processed the same downstream. Since these files were flagged temporary() before, they need to be recreated, thats why there might be some writing happening to the original directories
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nukappa
commented on September 4, 2024
But why not start after the final.bam files? avoids all unnecessary processing and proceeds with quantification of the DGE.
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