marianattestad / ribbon Goto Github PK

After cloning the repository as directed, I launch index.html in Firefox and it opens up and displays the index page. However, none of the dropdown menus display and none of the navigation links go anywhere.
I cloned the repo to my desktop (Windows 10) as well and it's behaving properly out of the box there. Links all work, dropdowns work.

Is there a requirement that I need for Linux? I didn't see anything specific listed just for running the software. Does index.html require specific permissions?

This is on Scientific Linux 7, accessing via xRDP.

Ribbon is a good tools to view SV.

Our bam was merged by multiple small bam file with more PG header.

Why do bam files with multiple @pg header lines have been found to have issues fetching records ?

Hi there,

I am trying to install Ribbon following the install steps on the github page but I get an error when running the last command:

esther@esther-ThinkPad-S3-Yoga-14:~/BAFSTU/LCAB/ribbon$ npm run build

[email protected] build /home/esther/BAFSTU/LCAB/ribbon
cat node_modules/{bootstrap/dist/css/bootstrap.min.css,jquery-ui-dist/jquery-ui.min.css} > css/bundle.css; cat node_modules/{d3/d3.min.js,jquery/dist/jquery.min.js,bootstrap/dist/js/bootstrap.min.js,@biowasm/aioli/dist/aioli.js,pako/dist/pako.min.js,moment/min/moment.min.js,jquery-ui-dist/jquery-ui.min.js} > js/bundle.js

cat: node_modules/{bootstrap/dist/css/bootstrap.min.css,jquery-ui-dist/jquery-ui.min.css}: No such file or directory
cat: node_modules/{d3/d3.min.js,jquery/dist/jquery.min.js,bootstrap/dist/js/bootstrap.min.js,@biowasm/aioli/dist/aioli.js,pako/dist/pako.min.js,moment/min/moment.min.js,jquery-ui-dist/jquery-ui.min.js}: No such file or directory

npm ERR! Linux 4.15.0-142-generic
npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "build"
npm ERR! node v4.2.6
npm ERR! npm v3.5.2
npm ERR! code ELIFECYCLE
npm ERR! [email protected] build: cat node_modules/{bootstrap/dist/css/bootstrap.min.css,jquery-ui-dist/jquery-ui.min.css} > css/bundle.css; cat node_modules/{d3/d3.min.js,jquery/dist/jquery.min.js,bootstrap/dist/js/bootstrap.min.js,@biowasm/aioli/dist/aioli.js,pako/dist/pako.min.js,moment/min/moment.min.js,jquery-ui-dist/jquery-ui.min.js} > js/bundle.js
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the [email protected] build script 'cat node_modules/{bootstrap/dist/css/bootstrap.min.css,jquery-ui-dist/jquery-ui.min.css} > css/bundle.css; cat node_modules/{d3/d3.min.js,jquery/dist/jquery.min.js,bootstrap/dist/js/bootstrap.min.js,@biowasm/aioli/dist/aioli.js,pako/dist/pako.min.js,moment/min/moment.min.js,jquery-ui-dist/jquery-ui.min.js} > js/bundle.js'.
npm ERR! Make sure you have the latest version of node.js and npm installed.
npm ERR! If you do, this is most likely a problem with the Ribbon package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR! cat node_modules/{bootstrap/dist/css/bootstrap.min.css,jquery-ui-dist/jquery-ui.min.css} > css/bundle.css; cat node_modules/{d3/d3.min.js,jquery/dist/jquery.min.js,bootstrap/dist/js/bootstrap.min.js,@biowasm/aioli/dist/aioli.js,pako/dist/pako.min.js,moment/min/moment.min.js,jquery-ui-dist/jquery-ui.min.js} > js/bundle.js
npm ERR! You can get information on how to open an issue for this project with:
npm ERR! npm bugs Ribbon
npm ERR! Or if that isn't available, you can get their info via:
npm ERR! npm owner ls Ribbon
npm ERR! There is likely additional logging output above.

npm ERR! Please include the following file with any support request:
npm ERR! /home/esther/BAFSTU/LCAB/ribbon/npm-debug.log

How do I fix this?

Kind regards,
Esther

Hi Maria,

Thanks for developing such a useful SV visualization tool. Is it possible to use this software to visualize fusions from Illumina short read RNA-seq data?

I filtered my BAM file to include only fusion supporting reads and then uploaded the filtered BAM into the public Ribbon web server. But I can seem to visualize only one chromosome or the other in my interchromosomal fusion. I had expected to find something similar to the example of PacBio CYTH1-EIF3H fusion ribbon plot, even though my reads are obviously much much shorter.

Looking at the same filter BAM file in IGV shows that there are spanning reads and junction supporting reads in the BAM file. So maybe I need some additional files to tell Ribbon what to visualize?

I attached the IGV and Ribbon plot from my fusion here, and the PacBio example I was referencing. Thanks in advance!

My Fusion in Ribbon

My Fusion in IGV

PacBio Example

Hello,

I wish to load SAM file which is larger than 10 MB, (and BAM file is larger, too).
I expected to do it when I download Ribbon locally but I did not manage.

Please help me.

Hi Maria,

First of all, thank you very much for providing Ribbon. I've found it being incredibly useful for my work in detecting complex genome rearrangements!

One feature that I think would be quite useful is to ignore the "small" gaps in long reads' alignments. This would get rid of the small indels that make the visualization a bit "too busy" for seeing the big picture (example with 3 alignments but several small gaps).

Thanks!

Steve

Hi Maria,

I tried to use Ribbon to visualize a large bam file from sniffle (22GB) with lots of structure variants, I uploaded the bam (with index) and bedpe files. But the fetching process for each location is more than several hours and I haven't been able to visualize any of them. I am aware that the file size may cause this problem, but do you have any suggestions for that issue? Is the only way I should do is to reduce the size and filter out unwanted reads?

Thanks!

Hello Maria,

I tried to upload a coordinate file (which has been attached) into Ribbon, but I have the following error message:

Error: The coordinates must be the same as MUMmer's show-coords -lTH. This means 11 tab-separated columns without a header:
Ref start
Ref end
Query start
Query end
Ref alignment length
Query alignment length
Percent Identity
Total reference length
Total query length
Reference name(chromosome)
Query_name

Would you look at my input coordinate file to see what was wrong with it?

Thank you in advance,

hoon

Hi Maria,

Awesome tool! Thanks for building it.

I have a question about permalinks. I've deployed a local copy and created a few permalinks. Then I realized that the data is available through your website http://genomeribbon.com/ too. Can you please explain how the permalink creation is configured? And, how can I delete my data that is in your servers? Also, is there a way that i can configure the permalink to write the data locally and access only locally?

Thanks in advance,
Cheers,
Sevgin

Dear Ribbon User and Developer,

What is the best way to convert the mummer alignment to bam, sam or mummer show-coords -lTH format. I have generated my nucmer alignment as follow:
nucmer --prefix=s3_cart myref.fna ../assembly.fasta

I convert the *detlta output to *coords as follow:
show-coords -ITH s3_cart.delta > s3_cart.coords

When I upload the is *coord file on Ribbon, I still have an error message regarding the formatting?

What is the best way I can get a ribbon compatible format with this with the nucmer or mummer output?

Cheers,
~DD

Hi Maria Nattestad,
Tanks for your useful tools Ribbon, the visualization looks pretty nice. But I want to know does it support vector graph output, like PDF/SVG format?
Best,
Brian

I am trying to load a mummer coords file produced in they way suggested, but on both the web version and the local version of ribbon, it tells me "Info: Loading a large file might take a while" and then after a few minutes the page dies. On Safari it just reloads and says "This page was reloaded due to an error" and with Chrome it says "Oh snap! Something went wrong while displaying this page"
The file is 25.1Mb and looks like this:

1682 1775 3 96 94 94 94.74 3862 106134 NODE_8182_length_3862_cov_69.738705 NODE_1_length_106134_cov_23.598508
1794 1883 2 94 90 93 93.55 3862 106134 NODE_8182_length_3862_cov_69.738705 NODE_1_length_106134_cov_23.598508
1837 1921 9 92 85 84 97.65 3862 106134 NODE_8182_length_3862_cov_69.738705 NODE_1_length_106134_cov_23.598508
498 670 9 175 173 167 79.77 692 106134 NODE_20591_length_692_cov_15.583740 NODE_1_length_106134_cov_23.598508
610 692 3 83 83 81 94.05 692 106134 NODE_20591_length_692_cov_15.583740 NODE_1_length_106134_cov_23.598508
8181 8239 14 71 59 58 94.92 20832 106134 NODE_879_length_20832_cov_22.150711 NODE_1_length_106134_cov_23.598508
8243 8390 95984 96131 148 148 88.67 20832 106134 NODE_879_length_20832_cov_22.150711 NODE_1_length_106134_cov_23.598508
2188 2263 9 84 76 76 96.10 2908 106134 NODE_9954_length_2908_cov_23.156835 NODE_1_length_106134_cov_23.598508
3902 3993 9 97 92 89 93.48 4062 106134 NODE_7871_length_4062_cov_21.663237 NODE_1_length_106134_cov_23.598508
2617 2698 9 95 82 87 93.10 3078 106134 NODE_9546_length_3078_cov_24.302233 NODE_1_length_106134_cov_23.598508
2928 3021 94 2 94 93 90.62 3078 106134 NODE_9546_length_3078_cov_24.302233 NODE_1_length_106134_cov_23.598508
1 106134 1 106134 106134 106134 100.00 106134 106134 NODE_1_length_106134_cov_23.598508 NODE_1_length_106134_cov_23.598508
1 10262 1 10262 10262 10262 99.96 106134 106134 NODE_1_length_106134_cov_23.598508 NODE_1_length_106134_cov_23.598508

Any advice would be appreciated

Thank you for your great tools. can you tell me how to remove expand regions from selected region. the red cycle part in the figure

Hi Maria,

Is the main website (http://genomeribbon.com/) down?

Thanks,
Matt

Hello,

I uploaded 'UCSC ref gene bed file' together with my coordinate file, and tried to filter only chr22' genes, but it does not work for me. A corresponding permanent link is:
http://genomeribbon.com/?perma=m9haulL2HO

I wonder if you can let me know how was wrong with me.

Thank you again,

Hi Maria, I seem to be having trouble loading a small bam (239 KB) and corresponding bai (400 KB) file into Ribbon with the Error: File taking too long to load. Any suggestions? Apologies if it's something simple, I'm quite new to the game.

Hi,

I am a fairly novice coder and was installing Ribbon after installing XAMPP v7.4.3. I followed the instructions and when I executed npm install, I got the following error message -bash: npm: command not found. I am not sure where npm is supposed to be located.

Thank you in advance for your help.

Hello Maria,

I expect that forward alignments would be colored with 'blue' and reverse alignments with 'red' in "multiread view", but I found that both were colored with 'blue' in my case.
Shown below are the single-read view for one reverse-aligned read and one forward-aligned read.
Would you let me know how to update the color setting?

Thank you in advance,

Hoon

Multiread view:

Dot plot for a reverse-aligned read:

Dot plot for a forward aligned read:

Hi,
I would really like to use ribbon to visualize my structural variants, but when I load the BAM and choose a location, I get back there are no reads in this location. I mapped PacBio files with NGMLR and they have a QNAME that follows this format @ /<ZMW_number>/_, but they do not include the chromosome. In your example you used PacBio alignments and did not have any problems, how did you get these to work? I've tried multiple aligners and the mapped BAM files always have the PACBIO BAM format as oppose to the conventional format.

hi, Ribbon is a great visualization tool. I am doing genome alignment using Mummer and have some questions.
I uploaded the mummer coords file following the instruction, but I found there are still many differences.


can you show me the command lines you used to get the gorilla_to_GRCh38.Assemblytics.10kb_min.coords? So I can the the same results like your example.
thank you!

I'm working on updating the Ribbon code to support the .CSI BAM indexing schema so I can use it with plant genomes containing chromosomes > 29^2-1 bp long.

I'm part way there already but I'm trying to figgur out what the BamFile.prototype.blocksForRange function is doing so I can update it to support CSI. Some pointers would be appreciated.

Dear author
I wonder how this software to use?The software I downloaded through the npm, but I don't know how to use it. I did n' t see any examples in the githup. Could you give me some instructions?
I don't know where to input and output files

Looking forward to your reply

Best
Tan

Hello,

I am using ribbon to confirm a possible inversion and I am excited about the options to visualize alignments. I am looking at a bam file, where I aligned pacbio data of an individual with one inversion haplotype to a reference that carries the other inversion haplotype.
If my target region is actually an inversion I expect to find more reverse mapping reads in that region compared to other regions of the genome. I want to test if I can see this in my data and would like to filter the reads based on length to focus on the longer ones and also the reads with higher quality. But if I add filter selections in the multiread settings (eg a minimum read lengths of 10kb) under the Reads tab this selection, that doesn't change anything in the output when I click go (to fetch my target region again with this filter). Meaning all shorter reads still occur in the output and the selection goes back to the default.
Does anyone know what could be going on? Does my request maybe take too much processing power for the program? My bam file has around 80GB and I am fetching an area with a 10kb margin to see the orientation of the longer reads more clearly.

I wanted to generate a permalink but the program currently throws an error when I try this (Error:undefined). Please let me know if I can provide any further information to the data I am working with.

Any advice to this or in general to confirm inversions with this program is very much appreciated!
Thank you in advance!
Hannah

Dear Maria,

Thank you for the great software.

In the plot generated by using mummer coordinates in genome ribbon, is there a way to increase the intensity of color of the lines between the two sequences?

Thank you,
Best,
Homa

Hi,
I am interested in using Ribbon. Would it be possible to upload the bam files from the server, if I host Ribbon in that server. Now even if I host ribbon in a server it is asking for files from my laptop. Since these are huge files, I have trouble in downloading them. I am not able to host the bam files publicly as well.

Thank you for your help! Please let me know if you need any other info.
Best,
Jainy

Hi i would like to use ribbon to view mummer alignments but cant get it to run.

Installed xampp and ribbon as described but get an "Object not found!" message when trying to query localhost/ribbon

I am currently running a webapollo instance on port 8085 to keep port 80 free.

Also do i have to start xampp for using ribbon (xampp start?). I did start it but got same "Object not found!" message.

Is there still conflicts between the appache services?
I am not familiar with webapplications at all so could you help me?

Thank you

Not sure why it doesn't like my bam files. They are pacbio aligned with ngmlr. The features are indesl from pbhoney and refflat is being used for genes.

Each chrom I select says no mapped reads.

Any ideas on how I can debug?

Let me first just say how useful this tool has been for our research.

I'm curious if there is a way to scale chromosomes by size when viewing MUMmer alignments? Currently both the top and bottom chromosomes are displayed with the same size horizontally even if they differ in size. We have several cases where a chromosome in one species is vastly larger than the corresponding chromosome in another species. It would be nice to be able to display the size difference when viewing the alignments. I don't think this is currently possible?

Hi Maria -

I installed Ribbon with no trouble. I'm trying to view a BAM file of PacBio reads aligned with BWA-MEM (its fairly small 1.4GB of a viral genome) I'm able to upload the BAM file and I can see the reference contig. When I type in a region (e.g. 10000). Then it hangs and I get a 'aw,snap' error in Chrome.

I tried loading the same BAM file in iobio and I get the same error message in Chrome. Do you have any idea what the issue might be? It seems like it can't read the BAM file for region of interest.

Hello Maria,

We are trying to use Ribbons for data analysis of viral integrations into the human genome sequence. Unfortunately, we have encountered an issue with one step of the analysis. Specifically, the MUMmer aligner is not recognizing the integration of the virus into the host genome. However, when we used an alternative program such as BLASTn, it was able to identify these regions. We used open-source data from a published article as a positive control, so those integrations exist.

I wanted to ask if you have had any experience editing the human reference genome (i.e. adding 3.2 -7kb extra sequence) for the MUMmer before and if the alignment program is the correct tool for identifying viral integration points. Any insights or suggestions you have would be greatly appreciated. Unfortunately, the authors of the aligner do not respond to the Issues section so I decided to contact you.

Thank you for your time and effort in developing Ribbons, did you consider using a different aligner prior to the visualisation of the chromosomal rearrangements or read-splitting, I found some people doing it for viral integrations.

Sincerely,
S-T-C

I'm often getting the "Aw, Snap!" error message on Chrome when it's Fetching.

Aw, Snap!
Something went wrong while displaying this web page.
Error code: RESULT_CODE_INVALID_CMDLINE_URL

Any tips on avoiding that?

Example case:
I'm loading a bam file (~ 400 Mb) & bai, then looking at a genomic position or clicking a variant from my vcf file, it's 'Fetching...', then crashes.

• I've checked that my file has a single @PG header line
• I've tried in Chrome incognito mode, if ever there was a cache issue.
• I wanted to try in Safari instead, but the file upload tool doesn't seem to display.

What am I doing wrong?

Hi, Maria. Bandage is astonishingly useful to me for visualizing misassemblies. Thanks for this tool!

I have a SAM or BAM file, and I'd like to programatically save an image of the top and bottom images, the bottom one a dot plot of a specified query sequence (or each of the query sequences, I'll have about ten or so). I'd like to upload the SAM/BAM file to http://genomeribbon.com using curl --upload-file and download a PNG/SVG/PDF. Alternatively a local installation of GenomeRibbon with a command line interface would work equally well. Any suggestions?

I tried to load my BAM files in various ways but they all failed

Thus, to check whether or not my BAM file is problematic, I tried BAM files from example data.

The example data I examined is "Illumina detection in A649 cell line (600KB)"

And the BAM file is
http://labshare.cshl.edu/shares/schatzlab/www-data/ribbon/DRR01684_merged.chr1.bam

But I was still unable to load the BAM file

how can i use Ribbon desktop/web version on linux, I tried with this current repository but unable to do so, is there any separate repository for that?

Hello,

I am trying to get Ribbon to work on Ubuntu 18.04.0 with sandboxed user account and no access to the internet.

The Ribbon webpage loads up fine, however nothing really happens when loading a pair of bam + bai files.
Looking at the Firefox developer console we can see the Uncaught TypeError: _CLI is null error popping up upon selecting the two files. Firefox version is 101.0.1 64bit.

The two files are located in a shared folder the user has R access to it.

I would really appreciate your help to figure this out and hopefully get it resolved. See the screenshot of the error below this message.

Regards