Dear all,
I have paired-end data of 150bp and i use bwa-mem to align it.
bwa-mem ref_genome R1.fq.gz R2.fq.gz > aligned_reads.sam
After the alignment, i have check the flags proportions and there is something that i do not understand, i have different count for sam flags 99/147 or 83/163.
99: 6239811
147: 6241593
83: 8113628
163: 8112417
This is the first time i have this, usually i get the same number of flags for 99/147 or 83/163.
Does it means that there is a problem during the alignment ?
Thank you for your help!
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written
by
Picoskia •
2 answers
[ Edited link (ATpoint) ]
the link is not working
Not sure which link @Buffo was trying to post but you can look at: https://www.samformat.info/sam-format-flag
thank you for the link but the thing that i do not understand is if a have a count of for example 2000 reads for sam flag 99 i should get also the same number of reads for its mate 147?
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