How can I find out reads with unique map and multiple map in BWA-MEM output?

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Samarth Kulshrestha

Thanks Mireya Plass.

And you have any idea about secondry alignment in MEM output?

coz XA tags represents sec alignment in ALN sampe algorithm.. any idea about MEM???

No issue. Actually i am looking for that only.

Sreeskandarajan Sutharzan

Did you search for the flag 0x0100?

Hello Sreeskandarajan.

Yes i follwed the link

http://picard.sourceforge.net/explain-flags.html

It explains sam flags. But still some confusion left in mind .

Gloria Broders

At the end of each sam line you will find two tags: AS and XS. This two tags will report the current alignment score and the secondary alignment score respectively. If both scores are the same, then you have a read with multiple optimal alignments .

Hi Samarth,

0x0100 means the alignment is not primary. See page 4 tutorial in the link given below.

http://www.embl.de/~rausch/sam.pdf