Total count of specific location on IGV

Question

[tylertibetli]

Total count of specific location on IGV is 12372 but when I look at the reads on IGV there are 251 reads,Do you know What is the problem?

Answer 1

[Samarth Kulshrestha]

According to IGV visualization settings, IGV displays a specified number of randomly sampled alignments configured by the downsampling parameters instead of keeping all of them in memory: You can check your IGV alignment display settings using Preferences window, click

• View>Preferences>Alignments.

Check the link for further clarification: https://software.broadinstitute.org/software/igv/Preferences

Check under the Alignments tab.

Hope this help.

[tylertibetli]

Dear Samarth,

Thank you for your assistance,

best regards,

Tyler