Dear all.
I use tophat to map RNA-seq data. After getting results, I use two ways to filter the alignment. one is using grep "NH:i:1" to get uniquely mapping reads; the other is using samtools view -bq to get reliable reads. However, I found many uniquely mapped reads have mapping quality =0. How to explain it?
It's a single-end data.
I use tophat to map RNA-seq data. After getting results, I use two ways to filter the alignment. one is using grep "NH:i:1" to get uniquely mapping reads; the other is using samtools view -bq to get reliable reads. However, I found many uniquely mapped reads have mapping quality =0. How to explain it?
It's a single-end data.
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