Hi, everyone!
I mapped a paired-end RNA-seq data with Tophat, but the properly paired reads is extremely little (about 5%), can anyone tell me what “properly paired” means and this 5% percentage means?
I filter the original .bam file accepted_hits.bam generated by Tophat with the following command:
samtools view - f 2 accepted_hits.bam -b > flt.bam
Thanks~
I mapped a paired-end RNA-seq data with Tophat, but the properly paired reads is extremely little (about 5%), can anyone tell me what “properly paired” means and this 5% percentage means?
I filter the original .bam file accepted_hits.bam generated by Tophat with the following command:
samtools view - f 2 accepted_hits.bam -b > flt.bam
Thanks~
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