How to confirm the mapped read sequence?

yyoshiaki / VIRTUS2

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.

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Closed km-2021 closed 2 years ago

km-2021 commented 2 years ago

Hi,

What is the best way to see read sequences mapped to the viral genome?

yyoshiaki commented 2 years ago

Hi,

you can check virusAligned.filtered.sortedByCoord.out.bam

ex.

samtools view virusAligned.filtered.sortedByCoord.out.bam

samtools view virusAligned.filtered.sortedByCoord.out.bam | less -S