majiq_voila

1–30 of 397

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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Dec 1

voila tsv error - more than one voila file found

Hello, newbie majiq user here. I have experiment with 4 groups and I've used the command_builder

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voila tsv error - more than one voila file found

Hello, newbie majiq user here. I have experiment with 4 groups and I've used the command_builder

Dec 1

Angel Liang, jai...@biociphers.org3

Dec 1

Missing read counts in splicegraph.sql

Also, you are not correctly pulling in read information in some locations. For example, one of the

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Missing read counts in splicegraph.sql

Also, you are not correctly pulling in read information in some locations. For example, one of the

Dec 1

zhenyu yang, … Paul Jewell6

Dec 1

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

Dec 1

Alexis W, Paul Jewell2

Dec 1

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

Dec 1

brown.a...@gmail.com, Paul Jewell2

Dec 1

How to use the incremental option on MAJIQ build

Hello, I am slightly confused by the exact sequence of events that took place. You may use

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How to use the incremental option on MAJIQ build

Hello, I am slightly confused by the exact sequence of events that took place. You may use

Dec 1

Aoi W., … Paul Jewell6

Dec 1

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

Dec 1

Hasna Khan, … Astrid D4

Nov 30

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

Nov 30

Angel Liang, Paul Jewell3

Nov 26

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

Nov 26

Nov 11

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

Nov 11

Maoting Chen, … Pavlína Věchtová5

Nov 3

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

Nov 3

George Tollefson, Paul Jewell2

Nov 1

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

Nov 1

George Tollefson, Paul Jewell2

Nov 1

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

Nov 1

Bea C, Paul Jewell2

Nov 1

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

Nov 1

Bea C, Paul Jewell2

Nov 1

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

Nov 1

Paula Navarrete, … Bea C5

Oct 27

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.

Oct 27

Onkar Mulay, jai...@biociphers.org2

Oct 25

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-

Oct 25

Onkar Mulay, Paul Jewell3

Oct 23

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,

Oct 23

Onkar Mulay, Paul Jewell2

Oct 15

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

Oct 15

Abby Feng, Paul Jewell2

Oct 15

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. (

Oct 15

Onkar Mulay, Paul Jewell4

Oct 15

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

Oct 15

Ruhi Naik, … Sean Murphy3

Oct 9

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

Oct 9

Max Ferretti, Paul Jewell3

Oct 8

"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:

Oct 8

Oct 8

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)

Oct 8

Nirad Banskota, Paul Jewell6

Sep 22

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

Sep 22

sushil, Paul Jewell2

Sep 13

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

Sep 13

mario.ke...@googlemail.com, … jai...@biociphers.org6

Sep 13

Cassette exon events lack second LSV

Dear Joseph and Matt, I checked the inidividual experiments for each of the two groups and found out

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Cassette exon events lack second LSV

Dear Joseph and Matt, I checked the inidividual experiments for each of the two groups and found out

Sep 13

Anna-Leigh Brown, … Paul Jewell6

Sep 10

Using strandness flag results in 0 LSVs, using strandness=none gives LSVs

As a follow up, this fix has worked for some others, so I've merged it back into master. You may

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Using strandness flag results in 0 LSVs, using strandness=none gives LSVs

As a follow up, this fix has worked for some others, so I've merged it back into master. You may

Sep 10

Chris Seward, Paul Jewell3

Sep 10

Missing major exon skipping event

Hello, I'm glad you were able to work out part of the issue. I wanted to mention that there was

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Missing major exon skipping event

Hello, I'm glad you were able to work out part of the issue. I wanted to mention that there was

Sep 10

Angel Liang, Paul Jewell2

Sep 10

majiq: command not found

Hello. The latest version of python we have officially tested is python3.8, so I would recommend

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majiq: command not found

Hello. The latest version of python we have officially tested is python3.8, so I would recommend

Sep 10

Olga Tsoy, Paul Jewell2

Sep 10

ImportError: ../lib/python3.7/site-packages/majiq/src/build.cpython-37m-x86_64-linux-gnu.so: undefined symbol: hts_tpool_init

Hello. From this is looks like the HTSlib integration had some issue. I would first recommend trying

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ImportError: ../lib/python3.7/site-packages/majiq/src/build.cpython-37m-x86_64-linux-gnu.so: undefined symbol: hts_tpool_init

Hello. From this is looks like the HTSlib integration had some issue. I would first recommend trying

Sep 10

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