Hi,
i checked the flags of a sam alignment file (paired end data) and i am a littte bit confused when i saw flags which are:
- read reverse strand, mate reverse strand, read mapped in proper pair (e.g. flag 115 or 179)
i thought that "read mapped in proper pair" means that in paired end data one read has to be on the forward and the other on the reverse strand, but in my example two reads are on the reverse strand and so i don't understand how to interprete this flag. Do i understand something wrong?
Thank you!
i checked the flags of a sam alignment file (paired end data) and i am a littte bit confused when i saw flags which are:
- read reverse strand, mate reverse strand, read mapped in proper pair (e.g. flag 115 or 179)
i thought that "read mapped in proper pair" means that in paired end data one read has to be on the forward and the other on the reverse strand, but in my example two reads are on the reverse strand and so i don't understand how to interprete this flag. Do i understand something wrong?
Thank you!