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alexdobin / STAR

RNA-seq aligner
MIT License
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reads without "vw" tag when use --waspOutMode #1640

Open Wen-ye1122 opened 2 years ago

Wen-ye1122 commented 2 years ago

Hi, when I use Star with the --waspOutMode option, I got a bam file. I found only around 10% of unique reads have a "vW:i:1" tag. According to the Star manual, the reads with "vW:i:1" are passed the WASP filtered. Other reads with the tag "vW:i:N" don't. but I still found some reads in my bam file. They didn't have a "vW" tag. I just want to know why they didn't have the "vW" tag and whether I should keep them or discard them in the next step.

alexdobin commented 2 years ago

Hi @Wen-ye1122

only reads that overlap variants go through the WASP algorithm, and get the vW tag. 10% seems like a reasonable proportion.