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yyoshiaki / VIRTUS2

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
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Query is marked as paired, but its mate does not occur next to it in your BAM file. Skipping. #24

Closed ppark123 closed 1 year ago

ppark123 commented 1 year ago

Hello, whenever I run any paired RNA-seq dataset including the sample ERR3240275 dataset, it outputs many of the same warning "*****WARNING: Query ERR3240275.162499 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping." with a different query number each time. I do get the same output as the table shown in the README.md, but will this have any effect on the final output of VIRTUS2?

yyoshiaki commented 1 year ago

Sorry for my late reply. You can ignore the warnings. In the later step, VIRTUS2 selects only paired reads.