majiq_voila

1–30 of 364

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

0 selected

Maoting Chen, Paul Jewell8

May 12

voila app error

Hi Maoting, Yay! I'm glad it was a relatively simple resolution afterall~ Thanks, -Paul On

unread,

voila app error

Hi Maoting, Yay! I'm glad it was a relatively simple resolution afterall~ Thanks, -Paul On

May 12

Juan Ferrer-bonsoms, jai...@biociphers.org2

May 6

change threshold in deltapi

Dear Juan, Are you getting the TSV output from majiq deltapsi directly? If not, you should be able to

unread,

change threshold in deltapi

Dear Juan, Are you getting the TSV output from majiq deltapsi directly? If not, you should be able to

May 6

Juan Ferrer-bonsoms, Paul Jewell4

Apr 28

sjdirs parameter majiq build

Hi Juan, Thanks for confirming it. May you try removing the 'readlen' and 'strandness

unread,

sjdirs parameter majiq build

Hi Juan, Thanks for confirming it. May you try removing the 'readlen' and 'strandness

Apr 28

Bruce Southey, Paul Jewell4

Apr 28

majiq build crash

Hi This is likely a memory-related bug exposed via aggressive gcc optimization. I had tried using a

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majiq build crash

Hi This is likely a memory-related bug exposed via aggressive gcc optimization. I had tried using a

Apr 28

li, Paul Jewell2

Apr 27

Copy LSV text below: empty when use voila view.

Hello Li, I believe this was a known older bug in Voila, and the issue was patched out in newer

unread,

Copy LSV text below: empty when use voila view.

Hello Li, I believe this was a known older bug in Voila, and the issue was patched out in newer

Apr 27

Elsa Claude, … Joseph Aicher5

Apr 23

LSV detected but STAR see no reads mapped to the corresponding gene

Wow, thanks a lot Jordi and Joseph. Your answers are exactly what I was looking for. I better

unread,

LSV detected but STAR see no reads mapped to the corresponding gene

Wow, thanks a lot Jordi and Joseph. Your answers are exactly what I was looking for. I better

pje...@biociphers.org

Apr 23

Justin Malin, Aicher Joseph5

Apr 10

apparent contradiction between Voila & IGV genome browser Sashimi plot

Hi Joseph, My apologies for the delayed response. Thanks very much for your helpful suggestion that

unread,

apparent contradiction between Voila & IGV genome browser Sashimi plot

Hi Joseph, My apologies for the delayed response. Thanks very much for your helpful suggestion that

Apr 10

huck.t...@gmail.com, Paul Jewell3

Apr 8

Lack of primers in MAJIQ-SPEL

Hi Paul, did you receive my emails? On Monday, April 5, 2021 at 9:18:04 PM UTC+1 Paul Jewell wrote:

unread,

Lack of primers in MAJIQ-SPEL

Hi Paul, did you receive my emails? On Monday, April 5, 2021 at 9:18:04 PM UTC+1 Paul Jewell wrote:

Apr 8

Rupert Hugh-white, … Elsa Claude11

Mar 31

LSV stringency parameters (min-experiments etc.)

Woops, actually this particular events has 11reads/3reads/7reads in 3 replicates for one condition

unread,

LSV stringency parameters (min-experiments etc.)

Woops, actually this particular events has 11reads/3reads/7reads in 3 replicates for one condition

Mar 31

Olga Tsoy, … Aicher Joseph3

Mar 26

Maximum junction lentgh

Just to add to Paul's answer, MAJIQ will not assign a junction to a gene unless its start and end

unread,

Maximum junction lentgh

Just to add to Paul's answer, MAJIQ will not assign a junction to a gene unless its start and end

Mar 26

Esther Kockelmans, … Paul Jewell41

Mar 26

MAJIQ voila error

Hi Esther, Could you post the run log for the `majiq build` step? I'm guessing the problem is

unread,

MAJIQ voila error

Hi Esther, Could you post the run log for the `majiq build` step? I'm guessing the problem is

Mar 26

Anna-Leigh Brown, salim megat4

Mar 19

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

Dear MAJIQ authors, just wondering if there is an answer to this question? On Tuesday, May 12, 2020

unread,

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

Dear MAJIQ authors, just wondering if there is an answer to this question? On Tuesday, May 12, 2020

Mar 19

shouvonik....@gmail.com, Paul Jewell3

Mar 19

Generating publication figures of the violin plots

Hi Paul, Sounds great! Thanks for the tip. Best, Nik On Friday, March 19, 2021 at 12:48:21 PM UTC-4

unread,

Generating publication figures of the violin plots

Hi Paul, Sounds great! Thanks for the tip. Best, Nik On Friday, March 19, 2021 at 12:48:21 PM UTC-4

Mar 19

huck.t...@gmail.com

Mar 18

Strandedness and number of exons

If a gene is on the "minus strand" of the mouse ENSEMBL genome annotation, does MAJIQ

unread,

Strandedness and number of exons

If a gene is on the "minus strand" of the mouse ENSEMBL genome annotation, does MAJIQ

Mar 18

Mar 17

reconciling Sashimi plot with MAJIQ splice graph

Hi, We are are trying to understand the difference in junctions reported by the MAJIQ splice graph

unread,

reconciling Sashimi plot with MAJIQ splice graph

Hi, We are are trying to understand the difference in junctions reported by the MAJIQ splice graph

Mar 17

Justin Malin, … Matthew Gazzara5

Mar 17

More exons than in annotation file

Hi Matthew, Great, that would explain it. Thanks for the explanation. I do have another question,

unread,

More exons than in annotation file

Hi Matthew, Great, that would explain it. Thanks for the explanation. I do have another question,

pje...@biociphers.org

Mar 17

Jon Gleur, Paul Jewell2

Mar 15

How to visualize http://localhost: files on a cluster?

Hi Jon, This is always possible, but it depends on your HPC administrator and their policies how

unread,

How to visualize http://localhost: files on a cluster?

Hi Jon, This is always possible, but it depends on your HPC administrator and their policies how

Mar 15

Oliver Ziff, … Paul Jewell5

Mar 15

LSV splicing type annotation

Hi All, I'm a little unsure of what the goal is in this case. The purpose of the "lsv_type

unread,

LSV splicing type annotation

Hi All, I'm a little unsure of what the goal is in this case. The purpose of the "lsv_type

Mar 15

Harvey Che, … Paul Jewell5

Mar 15

LSV found in voila tsv but not in voila view

Hi Else, splicegraph and deltapsi.voila files would be sufficient. Thanks, -Paul On Tuesday, March 9,

unread,

LSV found in voila tsv but not in voila view

Hi Else, splicegraph and deltapsi.voila files would be sufficient. Thanks, -Paul On Tuesday, March 9,

Mar 15

Pillai Lab, Paul Jewell2

Mar 15

Installation error on cluster

Hello, There is so much going on here, it will likely take a little while to Isolate all of the

unread,

Installation error on cluster

Hello, There is so much going on here, it will likely take a little while to Isolate all of the

Mar 15

Elsa Claude, Paul Jewell5

Mar 5

Calculation of psi when reference exon has a junction with the next exon (0 exon excluded)

Oh sorry that's my fault, I gave a deltapsi example, was not paying attention. Here is an example

unread,

Calculation of psi when reference exon has a junction with the next exon (0 exon excluded)

Oh sorry that's my fault, I gave a deltapsi example, was not paying attention. Here is an example

pje...@biociphers.org

Mar 5

Elsa Claude, Paul Jewell4

Mar 5

Chose one condition as control for deltapsi

Hi Elsa, No problem, I'm glad it's resolved. Thanks, -Paul On Friday, March 5, 2021 at 8:26:

unread,

Chose one condition as control for deltapsi

Hi Elsa, No problem, I'm glad it's resolved. Thanks, -Paul On Friday, March 5, 2021 at 8:26:

Mar 5

My Hoang, … jai...@biociphers.org8

Mar 1

No matching bam (and bam.bai) or sj file was found

Dear betsig, Could you provide more details (eg the log) about how MAJIQ fails when you try using it

unread,

No matching bam (and bam.bai) or sj file was found

Dear betsig, Could you provide more details (eg the log) about how MAJIQ fails when you try using it

Mar 1

Mar 1

Code from Vaquero-Garcia et al.

Hi, I wanted to ask if the code for generating Figure 4 from Vaquero-Garcia et al (eLife 2016) is

unread,

Code from Vaquero-Garcia et al.

Hi, I wanted to ask if the code for generating Figure 4 from Vaquero-Garcia et al (eLife 2016) is

Mar 1

Sarah Djeddi, Matthew Gazzara2

Feb 24

voila tsv output error

Hi Sarah, Thank you for your interest. To get a bit more information in order to help you out, can

unread,

voila tsv output error

Hi Sarah, Thank you for your interest. To get a bit more information in order to help you out, can

Feb 24

Alexis W, Matthew Gazzara6

Feb 24

Running MAJIQ PSI on replicates

Hi Alexis, Glad to have helped and thank you for using / improving the tool with your questions!

unread,

Running MAJIQ PSI on replicates

Hi Alexis, Glad to have helped and thank you for using / improving the tool with your questions!

Feb 24

Alexander Dietrich, Paul Jewell13

Feb 19

voila tsv error

Hello Alex, These column definitions were removed in general, we we ended up not fully trusting them,

unread,

voila tsv error

Hello Alex, These column definitions were removed in general, we we ended up not fully trusting them,

Feb 19

Huck Thornton, Paul Jewell2

Feb 17

Error in labeling samples in config file

Hi Huck, It's not just about the naming. You can specify names with the dpsi call, which will

unread,

Error in labeling samples in config file

Hi Huck, It's not just about the naming. You can specify names with the dpsi call, which will

Feb 17

tya...@gmail.com, Paul Jewell2

Feb 17

How to get gene name list sorted by the column "dpsi per junction" in interacting voila ?

Hello, I'm still a little unsure your desired use case / function. You would like voila TSV

unread,

How to get gene name list sorted by the column "dpsi per junction" in interacting voila ?

Hello, I'm still a little unsure your desired use case / function. You would like voila TSV

Feb 17

aykut sen, Paul Jewell3

Feb 15

Majiq psi - AttributeError: 'str' object has no attribute 'dtype'

Hi Paul, Thank you for your response and recommendations. The build command took about 4-5 minutes to

unread,

Majiq psi - AttributeError: 'str' object has no attribute 'dtype'

Hi Paul, Thank you for your response and recommendations. The build command took about 4-5 minutes to

Feb 15

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