Question: How to calculate the Average Insert Size after mapping the reads to the reference genome using BWA
0
gravatar for felipe_o_torquato
23 months ago by
felipe_o_torquato10 wrote:

Hi everyone,

Having mapped the reads (paired-end) to a reference genome using BWA, I am trying to check the mapping results.

Using the tool "Summary Statistics" it supposed to be possible calculate the average insert size (ISIZE - column 9 from the SAM file).

However, the ISIZE column presents positive and negative values. Thus, the average value is always zero since the negative values cancel out the positive ones.

How can I deal with these negative values?

size alignment insert mapping bam • 2.1k views
ADD COMMENTlink modified 23 months ago by Jennifer Hillman Jackson25k • written 23 months ago by felipe_o_torquato10
1
gravatar for y.hoogstrate
23 months ago by
y.hoogstrate460
Netherlands
y.hoogstrate460 wrote:

If I'm not mistaken, the tool "NGS: Picard: Collect Alignment Summary Metrics - writes a file containing summary alignment metrics" creates a figure showing the distribution of the insert size, maybe this helps...

ADD COMMENTlink written 23 months ago by y.hoogstrate460
1

CollectInsertSizeMetrics is also an option

ADD REPLYlink written 23 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 137 users visited in the last hour