majiq_voila

1–30 of 401

Hello everyone,

We just released a new update for MAJIQ 2 branch. MAJIQ 2.2 has a number of improvements and fixes in many edge cases during the majiq build process, as well as incremental build mode. In addition, there are small performance improvements, in majiq and voila and other new minor features.

Please see the full patch nodes and download details at the pinned thread here.

Thanks for your help and we hope you enjoy the new majiq, great new features are coming soon.

Biociphers Team.

------

Hello everyone,

MAJIQ 2.0 has been released. It represents a significant upgrade compared to previous MAJIQ 1.1. Main advantages and changes include:

A significant gain in speed. This is the result of algorithmic improvements and porting much of the core to C++.
New algorithm for intron retention. The new algorithm is both faster and more accurate.
New visualization engine: The release includes VOILA 2.0 which is now run as local service. This allows for smoother/faster interaction and enhanced features such as a built in search option.
Output a negative set: When comparing two conditions MAJIQ can give not only a high confidence set of changing events but also a high confidence set of events that are *not* changing.

As a consequence of these changes, MAJIQ 2.0 can easily handle hundreds and even thousands of samples. Most importantly, 2.0 serves as a base for many exciting new features and algorithms that support new use cases, so stay tuned!

Finally, while the academic license remains the same please note that commercial license has changed. Commercial users can keep using 1.1 as before, if they want to upgrade to MAJIQ 2.0 they should follow the instructions found on https://majiq.biociphers.org/commercial.php

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Jan 18

HET command usage

Hi, I do not fully understand how the heterogen command should be called. If I have several

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HET command usage

Hi, I do not fully understand how the heterogen command should be called. If I have several

Jan 18

Jan 14

ERROR: Failed building wheel for rna-majiq

I am attempting to install MAJIQ. I set up a conda environment with all of the dependencies installed

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ERROR: Failed building wheel for rna-majiq

I am attempting to install MAJIQ. I set up a conda environment with all of the dependencies installed

Jan 14

Jan 13

Failed Majiq installation due to python error.

Hello, I tried installing Majiq on a new Ubuntu machine but it failed. The output is: (env) (base)

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Failed Majiq installation due to python error.

Hello, I tried installing Majiq on a new Ubuntu machine but it failed. The output is: (env) (base)

Jan 13

Aoi W., Paul Jewell6

Jan 10

majiq build error: No matching bam

Hi Paul, Looks like that was it! Thanks! -Aoi On Mon, Jan 10, 2022 at 4:39 PM Paul Jewell <pjewell

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majiq build error: No matching bam

Hi Paul, Looks like that was it! Thanks! -Aoi On Mon, Jan 10, 2022 at 4:39 PM Paul Jewell <pjewell

Jan 10

Nicolas Gomez, … Joseph Aicher14

12/21/21

Segmentation fault: 11 on macOSm mojave 10.14.5

Amazing, thank you for the update! I am glad that you were able to get it working. Good luck with

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Segmentation fault: 11 on macOSm mojave 10.14.5

Amazing, thank you for the update! I am glad that you were able to get it working. Good luck with

12/21/21

brown.a...@gmail.com, Paul Jewell4

12/21/21

How to use the incremental option on MAJIQ build

Hello, I'm still slightly confused about exactly what happened. If you had a majiq build run that

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How to use the incremental option on MAJIQ build

Hello, I'm still slightly confused about exactly what happened. If you had a majiq build run that

12/21/21

Angel Liang, jai...@biociphers.org4

12/10/21

Missing read counts in splicegraph.sql

Thanks so much for the detailed reply! I appreciate it very much and I am sure that this will help

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Missing read counts in splicegraph.sql

Thanks so much for the detailed reply! I appreciate it very much and I am sure that this will help

12/10/21

Marek Schwarz, Paul Jewell2

12/2/21

voila tsv error - more than one voila file found

Hello Marek, Deltapsi mode works with one voila file at a time. When you specify just "/data/

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voila tsv error - more than one voila file found

Hello Marek, Deltapsi mode works with one voila file at a time. When you specify just "/data/

12/2/21

zhenyu yang, … Paul Jewell6

12/1/21

voila tsv error

Hi Hasna, It can range immensely. First by exons / junctions / intron count, and then more notably by

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voila tsv error

Hi Hasna, It can range immensely. First by exons / junctions / intron count, and then more notably by

12/1/21

Alexis W, Paul Jewell2

12/1/21

VOILA not compatible with Python > 3.9

Hello Alexis, The officially tested/supported version for majiq and voila is still python3.8 If you

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VOILA not compatible with Python > 3.9

Hello Alexis, The officially tested/supported version for majiq and voila is still python3.8 If you

12/1/21

Aoi W., … Paul Jewell6

12/1/21

Failed installation

Hi Aoi, This seems to still be a mac specific issue relating to xcode or search paths. I don't

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Failed installation

Hi Aoi, This seems to still be a mac specific issue relating to xcode or search paths. I don't

12/1/21

Hasna Khan, … Astrid D4

11/30/21

segmentation fault when running majiq build

Hi Astrid, I think for me the problem was arising because I generated my .bam files using a

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segmentation fault when running majiq build

Hi Astrid, I think for me the problem was arising because I generated my .bam files using a

11/30/21

Angel Liang, Paul Jewell3

11/26/21

Obtaining junction and intron read counts?

thank you! On Tuesday, 23 November 2021 at 2:11:28 am UTC+11 Paul Jewell wrote: Hello, There are read

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Obtaining junction and intron read counts?

thank you! On Tuesday, 23 November 2021 at 2:11:28 am UTC+11 Paul Jewell wrote: Hello, There are read

11/26/21

11/11/21

majiq build -- GFF format issue?

So, evidently the GFF files used directly from GENCODE (ie. https://www.gencodegenes.org/human/) work

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majiq build -- GFF format issue?

So, evidently the GFF files used directly from GENCODE (ie. https://www.gencodegenes.org/human/) work

11/11/21

Maoting Chen, … Pavlína Věchtová5

11/3/21

plot a 3D figure about the threshold and gene number

Dear Paul, Thank you so much for such a quick reply! It is a bit difficult for me to formulate my

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plot a 3D figure about the threshold and gene number

Dear Paul, Thank you so much for such a quick reply! It is a bit difficult for me to formulate my

11/3/21

George Tollefson, Paul Jewell2

11/1/21

Accessing Viola html without using local host

Hi George, There is no direct to HTML command as the browser is used for rendering the results, and

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Accessing Viola html without using local host

Hi George, There is no direct to HTML command as the browser is used for rendering the results, and

11/1/21

George Tollefson, Paul Jewell2

11/1/21

Error, Gene doesn't contain one of the Name attribute

Hello George, May you forward the link to the exact file you downloaded? I will see if I can

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Error, Gene doesn't contain one of the Name attribute

Hello George, May you forward the link to the exact file you downloaded? I will see if I can

11/1/21

Bea C, Paul Jewell2

11/1/21

HTML files from voila view?

Hi Beatriz, Voila has dynamic features (like changing / filtering splicegraphs, etc) so the entire

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HTML files from voila view?

Hi Beatriz, Voila has dynamic features (like changing / filtering splicegraphs, etc) so the entire

11/1/21

Bea C, Paul Jewell2

11/1/21

DB LSVs not reported in my results

Hello Bea, 1) Why are there only a few LSV's: From looking at the reads detected on the provided

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DB LSVs not reported in my results

Hello Bea, 1) Why are there only a few LSV's: From looking at the reads detected on the provided

11/1/21

Paula Navarrete, … Bea C5

10/27/21

GFF3 error: gene doesn't contain Name attribute

Hi Joseph, George and Paula, Thank George for your contribution with the last . I had the same Error.

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GFF3 error: gene doesn't contain Name attribute

Hi Joseph, George and Paula, Thank George for your contribution with the last . I had the same Error.

10/27/21

Onkar Mulay, jai...@biociphers.org2

10/25/21

Using psi.tsv for machine learning

Dear Onkar, psi.tsv provides rows per LSV, so quantifications are provided in terms of semicolon-

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Using psi.tsv for machine learning

Dear Onkar, psi.tsv provides rows per LSV, so quantifications are provided in terms of semicolon-

10/25/21

Onkar Mulay, Paul Jewell3

10/23/21

ERROR: sourc`e conflict: validate_and_build_gene

I have run the MAJIQ program successfully, thanks for the link Regards, Onkar On Friday, October 15,

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ERROR: sourc`e conflict: validate_and_build_gene

I have run the MAJIQ program successfully, thanks for the link Regards, Onkar On Friday, October 15,

10/23/21

Onkar Mulay, Paul Jewell2

10/15/21

sqlite3.IntegrityError: UNIQUE constraint failed: experiment.name

Hi Onkar, I think there should be more lines in this error -- I can not see the relevant part. Could

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sqlite3.IntegrityError: UNIQUE constraint failed: experiment.name

Hi Onkar, I think there should be more lines in this error -- I can not see the relevant part. Could

10/15/21

Abby Feng, Paul Jewell2

10/15/21

Error in running majiq DeltaPSI: IndexError

Hello, This most likely means that during the build step, for group C, there were zero LSVs found. (

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Error in running majiq DeltaPSI: IndexError

Hello, This most likely means that during the build step, for group C, there were zero LSVs found. (

10/15/21

Onkar Mulay, Paul Jewell4

10/15/21

Issue in running the program

Hello, Could you please try to do the two "module load" commands, before installing? On

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Issue in running the program

Hello, Could you please try to do the two "module load" commands, before installing? On

10/15/21

Ruhi Naik, … Sean Murphy3

10/9/21

Trouble Running MAJIQ Build

I have this exact same error where _GOMP_parallel was not found when running majiq build. I

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Trouble Running MAJIQ Build

I have this exact same error where _GOMP_parallel was not found when running majiq build. I

10/9/21

Max Ferretti, Paul Jewell3

10/8/21

"leaked semaphore" error when running voila

This worked great, thanks so much! On Friday, October 8, 2021 at 9:45:49 AM UTC-4 Paul Jewell wrote:

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"leaked semaphore" error when running voila

This worked great, thanks so much! On Friday, October 8, 2021 at 9:45:49 AM UTC-4 Paul Jewell wrote:

10/8/21

10/8/21

Hi, I wondered if it is possible to get the all the coordinates of only the green boxes (new exons)

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Hi, I wondered if it is possible to get the all the coordinates of only the green boxes (new exons)

10/8/21

Nirad Banskota, Paul Jewell6

9/22/21

When creating a gff file, should I filter out certain biotypes

Hello Paul, Thank you for that link. I don't understand though, for example, how MDM2 ended up

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When creating a gff file, should I filter out certain biotypes

Hello Paul, Thank you for that link. I don't understand though, for example, how MDM2 ended up

9/22/21

sushil, Paul Jewell2

9/13/21

BAM file, GFF3 file and Conf file.

Hello Sushil, I can help you with setting up the config file. The gff3 and bams are outside the scope

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BAM file, GFF3 file and Conf file.

Hello Sushil, I can help you with setting up the config file. The gff3 and bams are outside the scope

9/13/21

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