How To Upload Repeat Mask Fasta File On Igv (Integrative Genomics Viewer)

Question

[Hamilton]

Using IGV, I am trying to upload repeat mask fasta file with extension .out or .align as well as identified peaks of chipseq TF data to see whether detected peaks are called in repeated mask regions or not. When i tried, IGV does not allow to upload repeat mask file of fasta format.

do you know how to upload repeat mask file in IGV? do i need to convert it into other format? or, IGV is not doable to take a closer look at the repeated mask regions with detected peaks? anyone who tried this on IGV before?

any inputs are appreciated!

Answer 1

[marcosmorgan]

You can convert your .out file to a .gff3 file using the file converter provided by repeatMasker. Then you can load the .gff3 file to IGV.

You can get the converter from here. (Follow the installation steps 1 and 2 if you do not want to install and configure all repeatMasker).

Then from the folder where you have the .out file run:

$ perl /usr/local/RepeatMasker/util/rmOutToGFF3.pl myFile.out > myFile.gff3

Where myFile.out is the name of your file.

In the same folder where you have your .out file you will find the .gff3 file that you will be able to load to IGV.

NOTE: If your .gff3 file is big, it may freeze IGV. To avoid this, sort the .gff3 file using igvtools. Then, index the .sorted.gff3 file and finally load the .sorted.gff3 file. (You can find igvtools on Tools on the IGV menu bar).