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2019-01-30 07:42:46 -0600 received badge  Enthusiast
2018-10-10 08:01:37 -0600 commented answer Why does GenomeBrowse terminate when clicking to Plot icon?

Hi Tibor, It is possible, and the tricky thing with Linux is it is very hard for me to help reproduce / debug this. You may want to try updating to 18.04 (which the RHEL build works in our own testing). If that does not work, email me at my last name at goldenhelix.com

2018-10-09 08:41:58 -0600 commented answer Why does GenomeBrowse terminate when clicking to Plot icon?

Hi Tibor, We are looking at bundling changes to be more compatible with more versions of Linux (binary compatibility is like walking a tight-rope). One thing you can try is moving the bundled `lib/libstdc++.so.6` out of the way. That may allow GB to run with the RHEL binaries.

2018-10-05 11:45:18 -0600 answered a question Why does GenomeBrowse terminate when clicking to Plot icon?

HI Tibor,

It's unusual that this happened all of a sudden. There could be some issue with a file that the Plot dialog is trying to scan.

You can also try to install the RHEL version of GenomeBrowse, which we are considering making the default / only linux binary as it has been shown to be compatible with all linux distros:

http://www.goldenhelix.com/download/G...

Gabe

2018-09-10 01:57:46 -0600 received badge  Popular Question (source)
2018-09-04 10:31:48 -0600 edited answer HGMD integration

Hi Erin,

Please contact HGMD in terms of confirming if your licensed copy is available to integrate with any third party analysis solution.

Golden Helix has convert capabilities for standard genomic file formats such as BED/VCF for content that you own or have permission to use without restrictions inside third party tools.

Thanks, Jami...

2018-05-09 13:27:27 -0600 answered a question Error logging into GenomeBrowse with SSH handshake failed

Due to increased security requirements for connection to our login and upgrade server, existing GenomeBrowse installations (version 2.0.1 or newer) will fail to login with a red error message: “SSH handshake failed”. Unfortunately, for the same reason you will not receive the update notification for the recently released GB 3.0.0 that resolves this issue with an updated configuration.

You may find that GenomeBrowse continues to work for you if you had previously logged in and don’t log out, but please take the time to update to GenomeBrowse 3.0.0 to prevent any inconvenience and future interruptions.

Download and install GenomeBrowse 3.0 here: http://goldenhelix.com/products/Genom...

Thanks, Gabe

2018-05-09 13:26:39 -0600 asked a question Error logging into GenomeBrowse with SSH handshake failed

When logging in, I get a "SSH handshake failed" message!

2017-11-09 15:34:26 -0600 answered a question Stranded Paired-end RNA-seq coloring and wig/bw support

Hey Michael,

Thanks for the feature suggestions. The "first in strand" coloring sounds interesting and I see why it would be a helpful way to visualize reads. I have created a ticket to capture that coloring mode. We are not actively adding features to GB currently, but may in the future have a GB feature push.

We looked into bigwig support and even had an experimental version working. Unfortunately it's a pretty funky binary file format from the UCSC guys and we had a number of issues with it. We will revisit this at some point as well.

WIG files are actually supported by GB. You need to "convert" them first. Just select them in the Convert wizard (from the data manager or Plot window).

Thanks, Gabe

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2017-08-08 14:21:18 -0600 answered a question Tandem duplications in Illumina's paired end data

Hey Michael,

One mode that might be useful is to change the stacking mode to Paired End. If there is a tandem duplication, you may see it in the boundaries where paired-end reads that span it don't find the standard distribution for distance between the paired end reads or if there is an inversion you don't see one of a forward and reverse strand being paired.

Click the little gear icon in the GB Pile-up plot and switch Stack mode to Paired End.

I hope that helps! Happy hunting! Gabe

2017-08-08 14:09:01 -0600 answered a question Public annotations not loading

Hey Magnus,

I would try refreshing / restarting GenomeBrowse.

When we push updates to the repo, it may be down for a couple seconds and you can try to load at those unfortunate times.

At the moment I don't see any connectivity issues in our logs or from our environment.

Also, make sure you have updated proxy settings if necessary in your environment!

Thanks, Gabe

2016-11-01 10:00:45 -0600 answered a question Counting sense and anti-sense reads

Hey Ammar,

Our summary table here does not break out forward/reverse strand counts. Our default coloring scheme is based on forward/reverse mappings and there is also in the gear menu of the Pile-Up plot an option to "Split by Strand', which gives you a very nice visualization of strand-bias by placing all forward reads above and reverse reads below the axis.

image description

Example stacking:

image description

2016-01-20 13:27:03 -0600 answered a question How do I upload my 23 and me data to GenomeBrowse?

As an update to this, we now have native support for reading 23andMe files in GenomeBrowse!

Check out this YouTube video created by an avid GenomeBrowse user walking you through the process:

https://www.youtube.com/watch?v=ZHk4d...

Thanks, Gabe

2015-06-09 08:32:25 -0600 answered a question In Windows 7 x64 GenomeBrowse 2.0.7 freezes whenever I click within a track

Hey Beau,

I haven't been able to reproduce this on windows, so there might be something specific to the data or environment I'd like to track down.

But first, I'm going to send you an internal release for testing whether this has been fixed in our recent platform upgrade to Qt5 since our 2.0.7 release.

Thanks, Gabe

2015-06-05 11:18:25 -0600 answered a question Viewing Rearrangements in BAM files

Hey Brian,

I think your accurate in pointing out we don't have great support for investigating structural varinats currently. It's definitely something I'd like to improve.

A couple of things we are considering (feel free to comment/expanding on these):

  • Option to show soft and hard-clipped sequences when hovering over reads, allowing to see sequences at breakpoints.
  • Option to color reads by mate-pair distances, with a special color for mates on other chromosomes
  • Option to color reads with strand inversions from their mates
  • Option to have hover-labels configured to any of these useful properties (mates position, mate distances, etc)

Is there anything else IGV does to support this we should consider?

Thanks, Gabe

2014-09-12 14:13:16 -0600 answered a question I think the reference server's down?

Hey Eric,

Looks up to me. Could you let me know if there is a specific source that is having this issue?

Maybe post a screenshot.

Thanks, Gabe

2014-08-12 15:00:42 -0600 answered a question BAM format requirements

Right, for our network BAM file reading, we assume the .bai file is located at file.bam.bai rather than file.bai.

I'm sorry that that assumption doesn't hold up in your situation.

For local BAM files, we can look at the file system and see if there is no file.bam.bai but there is a file.bai we can find the index file and move on.

We can not generate .bai files for remote sources as that requires reading the entire BAM file (which is as much work as downloading the file).

2014-07-11 15:07:37 -0600 answered a question Crash when loading a BAM file in GenomeBrowse Win64 2.0.1

As an update

2014-06-11 09:48:04 -0600 answered a question GTF file cannot be uploaded

Hey An Hsu,

We don't allow plotting GTF files directly, but you should be able to convert them.

We decided not to display them in the Data Source Libraries view of plottable files in 2.0.2 since they are not plottable (that much has changed since 2.0.1)

But if you click on 'Convert', you should be able to Add your .gtf or .gtf.gz file and convert them into gene sources that you can use for plotting.

See our manual about converting GTF files.

Thanks, Gabe

2014-05-29 15:20:05 -0600 edited question Crash when loading a BAM file in GenomeBrowse Win64 2.0.1

Hi, I was trying to open BAM file in genomebrowser windows 64 bit version 2.0.1. But while doing that, the genomebrowser was shut down by itself every time. Does anyone has a solution for this?

Many thanks!

2014-05-29 15:18:05 -0600 answered a question bed file format for display transcripts

Hey An Hsu,

The BED format support in GenomeBrowse is focused around displaying "generic" intervals that have just a start, stop and potentially a label and color defined in the data.

If you actually have transcript data you want to display, I would suggest saving it out of UCSC in GTF format. The UCSC table browser should have a GTF export option.

Then our convert wizard will detect it as transcript data and you can visualize it as a Gene track.

Hope that helps, Gabe

2014-03-20 15:30:33 -0600 answered a question Symbolic link for bam files

Hey Enrique,

To answer your question from a Unix perspective: GenomeBrowse will see the file system like any other application and symbolic links are handled by the OS to look like the files they soft link to.

As long as the .bam and .bam.bai file are still side-by-side it shouldn't matter if they are being read through a symbolic link.

In fact, I use this quite a lot when testing etc.

Thanks, Gabe

2013-10-28 17:12:05 -0600 answered a question automatic snapshots

Hey Anne-Katrin,

We do have plans to add a "Save as Image" capability in our next major release of GenomeBrowse (version 2.0). We are working on the feature now actually, but the roadmap for it's release depends on a couple other dependencies and probably won't be for 2-3 months.

Although we don't intend to ship GenomeBrowse with a full Python API like we do with SVS, we do plan on providing a "remote control" mechanism similar to IGV's URL based control mechanism. This means you could have links like:

http://localhost:60151/goto?locus=egfr

To jump the running instance of GB to that location (which could be coordinates, not just a gene name). We could similarly provide a way to save an image such as:

http://localhost:60151/saveimage?out=somefile.png&width=600&height=480

You could then programatically construct and call these URLs to take snapshots of a list of loci as you are suggesting.

If having a more supported path to this functionality or an expatiated roadmap is something you are interested in, let me know as we have provided services to other labs looking for custom GenomeBrowse features and support and I'd be happy to chat and discuss the scope of that.

2013-09-30 08:44:55 -0600 answered a question BED files - RGB support

Hey Oswaldo,

We do support itemRgb. We expect the RGB colors to be encoded like numbers 200,0,0 (no parens).

We also expect the itemRgb="on" key/val pair on the 'track' line of the file. For example, here is a couple lines of a file that we render with color:

track itemRgb="On"
chr7    54028   73584   uc003sii.2  0   -   54028   54028   255,0,0 .   AL137655
chr7    60328   61569   uc010krx.1  0   -   60328   60328   255,0,0 .   PDGFA
chr7    62967   63529   uc003sij.2  0   -   62967   63366   255,0,0 .   DQ576410
chr7    64068   64107   uc003sil.1  0   -   64068   64068   255,0,0 .   DQ584609
chr7    65159   65220   uc003sim.1  0   -   65159   65159   255,0,0 .   DQ600587
chr7    75460   116489  uc003sin.1  0   -   75460   75460   255,0,0 .   AL137655
chr7    244679  249951  uc003sio.1  0   +   244679  244679  0,255,0 .   AK024243
chr7    244826  249951  uc010kry.1  0   +   244826  244826  0,255,0 .   AK310146

I hope that helps.

-Gabe

2013-05-22 21:19:05 -0600 answered a question How to visualize tandem duplications and translocations in GenomeBrowse?

Hey Bhakti,

Tandem Duplications may show up clearly in your alignments as either mismatches or large insertions, depending on your aligner's techniques.

Fusions may be a bit tricker to spot by eye, but fusion sites are often soft or hard clipped at the break point by the aligner for all spanning reads. It may look like a steep drop in coverage and the individual reads that you click on would show the clipping.

The evidence for fusion genes is almost always based on the paired-end alignments being one on each gene, and we don't provide a lot of support for visualizing that directly. If you go the gear menu in the pile-up plot and select to stack with paired-end matching, you will see pair-end reads that have their mate in a different chromosome or very far away in the same chromosome drawn with an arrow pointing towards their pair.

Another trick useful for this type of investigation is that you can open a second window on the same project from the Window menu. The second window can navigate to the second gene in the fusion event and by putting the windows side-by-side you can investigate the fusion.

But by the sound of your question, you might be searching for algorithms to detect tandem duplications and fusion events. If that's the case, I'm afraid GenomeBrowse won't be your final solution. GenomeBrowse is purely a visualization tool for existing data. If you have detected events, it's great at investigating their quality and genomic context, but it's not an analysis tool.

Thanks, Gabe

2013-04-30 21:06:46 -0600 answered a question Normalized display of RNA-seq data

Hey Irina,

I'm glad you have found GenomeBrowse useful!

There is no normalization of the coverage data per say, but notice that the Y axis auto-scales to the extents of your data. So two samples side-by-side will show a similar profile of exon coverage even if one has 10x as much data.

If you want the Y-axis to be set to the same scale, you can select multiple plots and edit the Y axis limits in the plot's control panel.

On your second question, we have plans for a more extensive "save image" feature, but for now we suggest taking a screenshot and cropping it to your relevant plots.

2013-04-30 21:03:35 -0600 answered a question Security of internal/proprietary data

Hey Rob,

I understand that this is a legitimate concern.

I can assure you that there no uploading of the contents of any of your data.

The purpose of the registration and account authentication is to allow for engagement through this community site and to have credentials for accessing secure cloud-based content (like our EA Pipelines and Illumina Basespace integration).

I have ideas about allowing for users to explicitly share projects and maybe even subsets of data as well through a cloud-based repository, but those of course would be things you opt in to very explicitly.

Thanks, Gabe

2013-03-25 08:09:13 -0600 answered a question BAM reader could not create index

Hey Tony,

Neanderthal Y-Chromosome! That sounds pretty neat!

That error is a internal one where the number of bytes we expect in a BAM block are more than the number we are able to read.

My guess is that the file might be truncated or corrupted.

If you would like us to take a look at the file, feel free to email us at genomebrowse@goldenhelix.com.

2013-02-07 09:01:13 -0600 answered a question HG19 genome

Hey Nick,

That's something we haven't run into, where you are able to download one of the example RNA-Seq samples but not annotations.

The "rfs://" versus "http://" is just protocol details but both the example samples and annotations are being served from the same host in the same manner (which is over HTTP port 80).

Could you double check that when on the Annotations tab, hitting the Refresh button doesn't pull in the source list for data.goldenhelix.com?

When you hover over the top level node that has the error, it should also display a tooltip with the details of why it was not able to connect. If you could post that as well it might help troubleshoot the issue.

Thanks!

2013-02-07 09:00:52 -0600 answered a question HG19 genome

Hey Nick,

That's something we haven't run into, where you are able to download one of the example RNA-Seq samples but not annotations.

The "rfs://" versus "http://" is just protocol details but both the example samples and annotations are being served from the same host in the same manner (which is over HTTP port 80).

Could you double check that when on the Annotations tab, hitting the Refresh button doesn't pull in the source list for data.goldenhelix.com?

When you hover over the top level node that has the error, it should also display a tooltip with the details of why it was not able to connect. If you could post that as well it might help troubleshoot the issue.

Thanks!

2012-11-29 16:35:17 -0600 answered a question Blank login window

Hey Kung-Hao,

I was able to reproduce the issue. It's very strange, but it caused by a dialog asking you if you want to continue because 1.0.5 is expired.

Unfortunately, 1.0.6 is not quite released (planned for next week) so the right thing to do is to tell it to continue.

But now you are faced with this weird separate bug of the dialog being blank! This seems to be Mac specific and we'll plan on fixing that in the future.

For now: There is a tricky work-around. When that blank dialog is up. Type Shift+Tab and then Enter. This essentially accepts the dialog and moves on.

Sorry for the inconvenience. We plan to have 1.0.6 out early next week.

2012-11-29 08:26:01 -0600 received badge  Civic Duty
2012-11-14 16:41:05 -0600 answered a question Not able to launch GenomeBrowse on Linux

Hey Manoj,

Unfortunately it can be difficult to build a single executable program that works perfectly well on every distribution of Linux. Unlike windows, each flavor of Linux has a different mix of standard libraries we depend on.

One thing to check is if you are running CentOS or Red Hat Enterprise Linux (RHEL) that you try our RHEL5 build of GenomeBrowse. The Lin64 build works on most modern Ubuntu/Debian distributions, but does has some known issues (including library incompatibilities that lead to Segmentation fault) on RHEL distros.

From our download page click the RHEL 64 download button and try that.

2012-10-12 12:17:36 -0600 answered a question BED file support

To expand on Jami's answer, although it's very enterprising to convert a BED file to BAM, the files have very different focuses on the types of data they support and the experience of viewing the converted data would be approximate at best.

Similarly, FASTA or GFF would not convert well to BAM. As Jami mentioned though, we plan on building built in support for converting all of these file types in the future.

For the moment, we are "bootstrapping" GenomeBrowse with the technology of SVS. This means for viewing annotation sources GenomeBrowse relies on annotations being converted to our efficient binary IDF file format.

SVS produces IDF files when converting BED, FASTA, GTF or any text file downloaded from the UCSC genome browser table viewer. GenomeBrowse is set up to auto-detect files that SVS converts, and they are ready to plot the next time you go to the Add dialog.

SVS is Golden Helix’s analysis product for a variety of workflows and is a commercial tool, you can request an evaluation of SVS through the evaluation request form.

2012-10-12 12:05:22 -0600 commented answer BED file support

Sara, I'm sorry to hear you ran into a crash. We are trying to collect examples of BAM files that do cause crashes.

Please email us at genomebrowse@goldenhelix.com if you would be willing to share the BAM file you created in a secure fashion.

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2012-10-01 20:44:08 -0600 answered a question Login and Account Requirements

The registration and login process is used to authenticate you to the GenomeBrowse cloud annotation server and to keep the software up to date by checking for updates.

Also, your GenomeBrowse account is used to log you into this Q&A site!

2012-10-01 20:37:24 -0600 answered a question BAM format requirements

We require the BAM file be sorted, that's it.

Often, pipelines that write bam files also write the bam index (BAI) file alongside it. Great!

If the BAI file is available, we will use it and you can immediately view the reads below the 10kb zoom window while we compute coverage data above that threshold.

If no BAI file is preset, we compute both the BAI and the coverage data in one pass.

Unfortunately, until that compute is finished, it's not possible to read any data in genomic coordinates and thus you won't be able to see any reads at any zoom level.

2012-10-01 20:32:29 -0600 answered a question Window size

Yes, there is a zoom limit above which we switch the rendering into a mode that shows strand-colored coverage and maximum depth, gapped alignments and mismatches in the coverage and pile-up plots respectively.

If you are seeing the "Data is unavailable at this zoom level." we were not able to build the "coverage data" file for your source. This is most likely because the BAM file your are viewing was not in a writeable location or you canceled the background task of computing that coverage.

Note that even while that background task is running, you can always zoom below the threshold to see pile-up data.

2012-10-01 20:28:38 -0600 answered a question File size limit

We have designed GenomeBrowse to scale wonderfully to whole genome DNA-seq data, and there are no hard-coded limits on file size or read density or pretty much anything.

What generally becomes the constrained resource in any big-data visualization system is how much data you can hold in RAM to render your plots in full detail.

Even here we have worked to make the worst-case scenario of millions and millions of reads in a small (<10kb) window at least not break GenomeBrowse. Instead, we drop some reads from the pile-up plot while continuing to count them in the coverage plot. You will get a little warning icon on the bottom of your pile-up plot if you do ever get to such a high-density region.

If you experience any failures to handle large files, we would consider it a bug. In such cases we ask for your help if at all possible to share your data securely so we can reproduce and resolve the issue.

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2012-09-26 10:59:40 -0600 asked a question aaaaaaaaaaaaaaa a

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2012-09-25 22:56:05 -0600 asked a question Host Not Found when trying to Register

Thank you very much for the links. However I am not been able to run the program after installing. It is telling host not found. Please advice some solutions of this problem.