Whit Athey's profile - activity

I have used the GH browser successfully on a number of BAM files. Now I have a genome in CRAM format and I can't seem to do anything with it. GH apparently won't load it. I can not understand the unix tools that may be available for converning files. Is there any simple way around this problem? Is there any way to make GH recognize and load a CRAM file? Maybe I don't have the most recent version?

This error occurred during the computation of the BAI index.

What exactly does the brown shading in a sequence represent? The annotation just says "Reference Match", but most of the sequence where it matches the reference, the bases are colored as one of the four primary colors. Is the brown shaded base in the sample sequence or not?

Or, if the brown shading really does indicate a match to the reference sequence being used, why are not all of the matching bases colored brown. In my plot, only about 20% of bases are brown, even though all of them match. About 80% are getting the red-blue-yellow-green shading as though they were variants. How can I have only actual variants being colored different from brown?

Never mind--I have found my problem--I wasn't using the appropriate reference--the "Match" is just the normal indication and is colored brown. The coloration is just for variants.

Correction: where I wrote "Read Depth 14" in the third sentence, it should have been "Match Depth 14".

At some locations the consensus base call in the "Read Depth" track is colored brown (it seems to match the reference). The corresponding strands in the "Pile Up" track do not show a base call. In the "Read Depth" track, a mouse-over of the base shows (for example) "Read Depth 14". When the base in the "Read Depth" track is colored one of the four colors, a mouse-over shows something like "C Depth 15". What is the difference between "Match Depth" and normal read depth? Is the distinction between the colored or brown locations something assessed and added by the browser or is it something from the BAM file? Why would the property causing the brown coloring be uniform across all the strand reads?

And, I can now have both references displayed without killing the display of my data. I'm not sure I understand what's going on, but I have obtained the information I was looking for. Thanks!

I can now see both files displayed as they should be. It apparently did have something to do with the reference, but it wasn't clear just what. I removed the hg19 reference and put in the g1k reference, but at first nothing happened. Then I swapped them again and it started working with either.

According to the company that produced the above-mentioned mtDNA BAM files, the read depth is about 2000X. Is that too much to be displayed in the GH browser? Could that be causing the problem?

I am trying to display and compare two mtDNA sequences and also the reference sequence. The reference sequence is showing just fine, but the plots for my two BAM files are blank. Since the reference sequence is showing individual bases, I assume my scale is okay. The two files seem to load okay, and the titles of the files are showing, but no data. How do I get the plot to show up?

I am not interested in comparing to some particular transcript, but rather to the consensus reference (forward) sequence. How can I force the browser to use this reference? I have already selected HUGO v 105 in the upper left pane--isn't that what I want?

I am new at this, obviously, but now I see that in the reference pane I have a transcript from some publication that happened to sequence the reverse strand. That undoubtedly forced the view of my own sequence in the top pane to also be the reverse (negative) strand.

I am using GH version for Win 7 (64) downloaded Dec 2015