IGV interval remove read

[Wei Tang]

Hi IGV Team,

I used IGV 2.1.21 version to visualize two bam files from TopHat aligner. As the picture I attached, I found for the 2nd sample, IGV automatically removed 149 reads in a interval, highlighted by a black frame.

I wonder what is the criteria for the filtering, and where I can change the parameters.

Thank you very much.

Wei

NCI/NIH

[Jim Robinson]

Its just indicating that the region was downsampled, and 149 reads were removed in the process.  You can change sampling parameters from the preferences window, or turn off sampling altogether.  If you do,  IGV could freeze in regions of very deep coverage, so its best to just increase the limits rather than turn it off.

Select View > Preferences > Alignments tab.  Sampling paramters are at the top.  See the user guide for more details.

Jim

[Wei Tang]

Clear, many thanks, Jim!

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