majiq_voila

1–30 of 378

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

Paula Navarrete

8:31 AM

GFF3 error: gene doesn't contain Name attribute

Hi, When I run majiq build command with gff3 file downloaded from ensembl, which contains the Name

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GFF3 error: gene doesn't contain Name attribute

Hi, When I run majiq build command with gff3 file downloaded from ensembl, which contains the Name

8:31 AM

Sep 14

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

Hello, I notice that some genes have exons more than they should have. I feel that it is related to

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

Hello, I notice that some genes have exons more than they should have. I feel that it is related to

Sep 14

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

unread,

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

joshy45266, Paul Jewell2

Sep 10

Failed Installation

Hello, The specific error leads to "Something's broken. UCHAR_MAX should be defined in

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Failed Installation

Hello, The specific error leads to "Something's broken. UCHAR_MAX should be defined in

Sep 10

santosh, Paul Jewell2

Sep 10

NameError: name 'pickle' is not defined

Hi Santosh, Reviewing this error message, I believe this specific internal function has been

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NameError: name 'pickle' is not defined

Hi Santosh, Reviewing this error message, I believe this specific internal function has been

Sep 10

Elton Vasconcelos, Jordi Vaquero2

Aug 12

Installation failure: ** Segmentation violation signal raised. **

Hi, sorry for the problem. Magiq has not been tested for intel compiler, but for gcc and clang. Is

unread,

Installation failure: ** Segmentation violation signal raised. **

Hi, sorry for the problem. Magiq has not been tested for intel compiler, but for gcc and clang. Is

Aug 12

Jul 6

bash: majiq: command not found

I think MAJIQ will not work in the environment created by Conda. This problem has been solved since I

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bash: majiq: command not found

I think MAJIQ will not work in the environment created by Conda. This problem has been solved since I

Jul 6

Jun 29

plot a 3D figure about the threshold and gene number

Hi, Just to add on to my question. In Voila view html file, we can adjust the threshold of the dPSI

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plot a 3D figure about the threshold and gene number

Hi, Just to add on to my question. In Voila view html file, we can adjust the threshold of the dPSI

Jun 29

Greg Chik, Matthew Gazzara2

Jun 15

Single-end reads for MAJIQ

Hello and thanks for your interest. Paired-end reads tend to be better just because they generally

unread,

Single-end reads for MAJIQ

Hello and thanks for your interest. Paired-end reads tend to be better just because they generally

Jun 15

Jun 14

Question about the group mean psi value from the output of majiq dpsi

Hi all, I have a question about how the group mean psi values from the output of majiq dpsi were

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Question about the group mean psi value from the output of majiq dpsi

Hi all, I have a question about how the group mean psi values from the output of majiq dpsi were

Jun 14

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

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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

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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

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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

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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

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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

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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:

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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

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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

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MAJIQ voila error

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

Mar 26

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

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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

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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,

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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

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