Question: Secondary Alignment in BAM flag
1
gravatar for eudoraleer
3.7 years ago by
eudoraleer10
Singapore
eudoraleer10 wrote:

Hi all, was wondering what does it mean by secondary alignment in BAM flag? 

What is been defined as unmapped reads?

Option used:

samtools view -F 260 bam_file

 

Thanks!

bam sequence alignment • 5.1k views
ADD COMMENTlink modified 3.7 years ago by Devon Ryan91k • written 3.7 years ago by eudoraleer10
6
gravatar for Devon Ryan
3.7 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

Unmapped reads are in the BAM file but have no valid assigned position (N.B., they may have an assigned position, but it should be ignored). It's typically the case that a number of reads can't be aligned, due to things like sequencing errors, imperfect matches between the DNA sequenced and the reference, random e. coli or other contamination, etc..

A secondary alignment occurs when a given read could align reasonably well to more than one place. One of the possible reported alignments is termed "primary" and the others will be marked as "secondary".

ADD COMMENTlink written 3.7 years ago by Devon Ryan91k

Thank you Ryan, I have a small question, are secondary aligned reads considered duplicates?

ADD REPLYlink written 3.7 years ago by eudoraleer10
1

I assume you mean PCR duplicates, to which the answer is no.
 

ADD REPLYlink written 3.7 years ago by Devon Ryan91k

Thanks, I think I am getting too confused with the terms duplicates, coverage and secondary reads, especially between duplicates and coverage, explanations in many posts does not seem to get me fully understood the meaning of pcr duplicates.

ADD REPLYlink written 3.7 years ago by eudoraleer10
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