Question: Identify how many inserts mapped to a region
gravatar for emmylou.nicolas
12 months ago by
University of Adelaide
emmylou.nicolas0 wrote:

Hi, good day. I am struggling looking for the insert mapped in my alignment.

I did this samtools view SRR5882792_thaliana.bam 2:15186040-15186852 | head

I saw in the CIGAR table that there are only perfect matches like 100M but none with I which indicates insertion

I just wanna ask if the insert mapped is the same as insertion?

or is there any other way to find the insert mapped in a bam file?

Thanks :)

ADD COMMENTlink written 12 months ago by emmylou.nicolas0

What's your understanding of "insert mapped"?

ADD REPLYlink written 12 months ago by finswimmer13k
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