SMRT sequence data visualization

[conr...@mail.usf.edu]

Hi,
I'm new to genomic data visualization and I've been trying to find a way to visualize genomic methylation and search for genes that contain specific methylation motifs. I have single molecule real time sequencing data (SMRT) and have run a basic modification and motif analysis using SMRT analysis. Using IGV I've been able to import the de novo assembled genome with two chromosomes (fasta), a rast annotated version of the genome(gff), and from SMRT analysis the x_modifications.gff file. The problem is that all the base modifications are shown, most of which are artifacts. My questions are: is there a way to filter the base modification track?, can I search for specific motifs (a list is generated using SMRT analysis), and can I search the annotation track for specific genes that I know the name  of (so I can view methylation of the gene)? Also, the Find Motif function does not work after I have entered a sequence. It returns "Please enter a search pattern" regardless of the text entered.  I am using IGV 2.3.88.
Thanks for the help.

[Helga Thorvaldsdottir]

Hi,

-Based on the screenshot, it looks like you want to filter out from view certain features in the gff file. IGV cannot do that, so you would need to filter the file before you load it.

-You can search for features that are present in a loaded annotation file by entering the feature name in the search / genomic locus box in the toolbar, as long as it's not an indexed file.

-The Find Motif function is working for me in IGV 2.3.88. Do you remember which sequence you tried? Or can you send us your igv.log file (or at least the part of it that covers the session when you were using the function) so we can try to figure out what's going on.

Helga

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[conr...@mail.usf.edu]

Hi Helga,
Thanks, I didn't know how to search but found the window. The problem with the motif finder was resolved, the text box where you enter the motif was not visible and I had tried entering the information in the +/- strand boxes.
James

[Helga Thorvaldsdottir]

Thanks for the update.

Helga

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/fa06d4aa-b2d0-4a9b-88cd-c4fb1d7a9c8b%40googlegroups.com.

[Helga Thorvaldsdottir]

James,

One more thing, if you again run across the issue of the text box not being visible, can you send us a screenshot.

Thanks,
Helga

[conr...@mail.usf.edu]

Helga,
I found out the problem was not with the program displaying the text box but the color of it was not showing up on one of the monitor I am using. When I pasted the screenshot onto my secondary monitor the text box was clearly visible.
Thanks for your help,
James C.

[Helga Thorvaldsdottir]

James,

Good to know. Thanks.

Helga

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/9470da0a-627a-4980-aa62-df3a30744183%40googlegroups.com.