trinityrnaseq-users

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As of mid-2024, Trinity RNA-seq project no longer has dedicated funding for future development, maintenance, or support. Please kindly consider this as you post issues or are in search of assistance.

There's a *lot* of documentation here in the forum and in github, so if you encounter trouble that has been addressed before by others, be sure to leverage this available knowledgebase to troubleshoot issues.

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Kishor Kumar Sarker, Brian Haas2

May 25

understanding edgeR results

Hi Kishor, Be sure to use the counts matrix as input to the DE analysis. There should be an R script

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understanding edgeR results

Hi Kishor, Be sure to use the counts matrix as input to the DE analysis. There should be an R script

May 25

Kishor Kumar Sarker, Brian Haas3

May 15

Hi, For the singularity installation, try this assuming linux: https://docs.sylabs.io/guides/3.0/user

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Hi, For the singularity installation, try this assuming linux: https://docs.sylabs.io/guides/3.0/user

May 15

May 15

Facing the issue while using RSEM

I am a new to bioinformatics , when i performing DenovoRNAseq while performing abundance estimate

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Facing the issue while using RSEM

I am a new to bioinformatics , when i performing DenovoRNAseq while performing abundance estimate

May 15

May 10

error occur while perform the assembly creation using trinity.

i am run this command. /mnt/e/DenovoRNAseq/TOOLS/Trinityrnaseq-v2.6.6/Trinity --seqType fa --left

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error occur while perform the assembly creation using trinity.

i am run this command. /mnt/e/DenovoRNAseq/TOOLS/Trinityrnaseq-v2.6.6/Trinity --seqType fa --left

May 10

May 10

Hi everyone, I have assembled some RNA seq reads using trinity and did the DE analysis with Salmon

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Hi everyone, I have assembled some RNA seq reads using trinity and did the DE analysis with Salmon

May 10

May 6

Trinity RNA-seq project no longer has dedicated resources

As of mid-2024, Trinity RNA-seq project no longer has dedicated funding for future development,

unread,locked,

Trinity RNA-seq project no longer has dedicated resources

As of mid-2024, Trinity RNA-seq project no longer has dedicated funding for future development,

May 6

May 6

Hey all, I am currently using trinity with the same parameters i used previously with my old samples

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Hey all, I am currently using trinity with the same parameters i used previously with my old samples

May 6

Holly Williams, Brian Haas2

Apr 20

shrink log fold change option in Trinity pipeline?

Hi, The trinity script doesn't run shrinkage of LFC if it's not part of the default

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shrink log fold change option in Trinity pipeline?

Hi, The trinity script doesn't run shrinkage of LFC if it's not part of the default

Apr 20

アレルギー万年

Apr 16

--no_symlinks Error

Hi there, I tried to run the trinity v2.15.1 with only one RNA seq data. (paired end reads. total 2

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--no_symlinks Error

Hi there, I tried to run the trinity v2.15.1 with only one RNA seq data. (paired end reads. total 2

Apr 16

Mar 21

Hello! I'm running trinity on multiple samples with an array job and I seem to be having issues

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Hello! I'm running trinity on multiple samples with an array job and I seem to be having issues

Mar 21

Hu Wang, … Janay Fox3

Mar 18

add --rg_sample for SNP calling

Ohhh I realize now I did the same thing since I thought the -S option would indicate sample files for

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add --rg_sample for SNP calling

Ohhh I realize now I did the same thing since I thought the -S option would indicate sample files for

Mar 18

Janay Fox, Brian Haas3

Mar 15

SJ output too small Variant calling

Oh great, running the script on the singularity image worked! Thank you so much! On Friday 15 March

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SJ output too small Variant calling

Oh great, running the script on the singularity image worked! Thank you so much! On Friday 15 March

Mar 15

Emily Kunselman2

Mar 8

issue installing goseq in R for use with analyze_diff_expr.pl

Update: I was able to install all necessary R packages. I am having an issue running

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issue installing goseq in R for use with analyze_diff_expr.pl

Update: I was able to install all necessary R packages. I am having an issue running

Mar 8

Mar 6

Trinity disk quota error

Hi there, I am attempting to use Trinity to do a large metatranscriptomic co-assembly (~420 M read

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Trinity disk quota error

Hi there, I am attempting to use Trinity to do a large metatranscriptomic co-assembly (~420 M read

Mar 6

Mar 4

Variant calling on multiple samples

By the way I got the option to work so to anyone who is wondering the option is still available! On

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Variant calling on multiple samples

By the way I got the option to work so to anyone who is wondering the option is still available! On

Mar 4

Mar 4

Weird pattern showing up in log2 FC plots

Hi, Sorry if this is too unrelated but I have been trying to search up a potential answer as to why I

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Weird pattern showing up in log2 FC plots

Hi, Sorry if this is too unrelated but I have been trying to search up a potential answer as to why I

Mar 4

Emily T, … Lada Jovović5

Feb 20

multi species comparative transcriptomics and differential expression analyses

Hi Mark, thanks again for linking your paper. I've now assembled my species specific

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multi species comparative transcriptomics and differential expression analyses

Hi Mark, thanks again for linking your paper. I've now assembled my species specific

Feb 20

Banisha Phukela

Feb 15

Dear Trinity users, I have tried to run trinity file for de novo seq assembly. I got an error which i

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Dear Trinity users, I have tried to run trinity file for de novo seq assembly. I got an error which i

Feb 15

Feb 13

Trinity.tmp.fasta

Hi guys, Before, I used older Trinity versions and now I switched to the latest Trinity-v2.15.1 so

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Trinity.tmp.fasta

Hi guys, Before, I used older Trinity versions and now I switched to the latest Trinity-v2.15.1 so

Feb 13

Abdel M A Hans YAYA-OYE, Brian Haas2

Jan 25

Exception : [unrecognised option '--minAssignedFrags']. Exiting.

Hi, If you're not using a recent version of salmon, then that could be the problem. Try running

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Exception : [unrecognised option '--minAssignedFrags']. Exiting.

Hi, If you're not using a recent version of salmon, then that could be the problem. Try running

Jan 25

Rob W., Brian Haas4

Jan 4

Trinotate: incorrect paths to perl scripts looking for /util/admin

Hi Rob, When you're in the Trinotate shell with the singularity image, then just execute the

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Trinotate: incorrect paths to perl scripts looking for /util/admin

Hi Rob, When you're in the Trinotate shell with the singularity image, then just execute the

Jan 4

Kishor Kumar Sarker, Brian Haas4

12/27/23

DE analysis with a genome guided approach

Yes, align then merge then assemble. best, Brian On Wed, Dec 27, 2023 at 9:17 AM Kishor Kumar Sarker

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DE analysis with a genome guided approach

Yes, align then merge then assemble. best, Brian On Wed, Dec 27, 2023 at 9:17 AM Kishor Kumar Sarker

12/27/23

Nishant Raj, Brian Haas2

12/26/23

Trinotate report with empty all columns

Hi, This happens when the boilerplate wasn't initialized properly via the Trinotate --create

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Trinotate report with empty all columns

Hi, This happens when the boilerplate wasn't initialized properly via the Trinotate --create

12/26/23

12/26/23

Trinotate report with all empty columns

Hi all, I completed all steps of Trinotate annotation successfully, But the annotation report created

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Trinotate report with all empty columns

Hi all, I completed all steps of Trinotate annotation successfully, But the annotation report created

12/26/23

David Bradshaw, Brian Haas9

12/17/23

Collapse genes based upon trinnotate annotation

Sure thing. Best of luck! On Fri, Dec 15, 2023 at 7:36 AM 'David Bradshaw' via trinityrnaseq-

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Collapse genes based upon trinnotate annotation

Sure thing. Best of luck! On Fri, Dec 15, 2023 at 7:36 AM 'David Bradshaw' via trinityrnaseq-

12/17/23

berger juliette, Brian Haas2

12/17/23

filter_low_expression

After filtering the Trinity.fasta to generate a new fasta file, you can redo the quantification (in a

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filter_low_expression

After filtering the Trinity.fasta to generate a new fasta file, you can redo the quantification (in a

12/17/23

berger juliette, Brian Haas2

12/17/23

filter_low_expr_transcripts.pl

Yes, if you filter the Trinity.fasta to make a new one, then use that new one for downstream analyses

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filter_low_expr_transcripts.pl

Yes, if you filter the Trinity.fasta to make a new one, then use that new one for downstream analyses

12/17/23

Laia Leria Florensa

12/15/23

Error after Phase 2

Dear Brian, I have found this error at the end of Phase 2 of the assembly and I have no idea how to

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Error after Phase 2

Dear Brian, I have found this error at the end of Phase 2 of the assembly and I have no idea how to

12/15/23

Rob W., Brian Haas6

11/30/23

Disk quota exceeded during phase 2 assembly of clustered reads

Fantastic! I always love hearing about when things work! :-) all the best, Brian On Thu, Nov 30, 2023

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Disk quota exceeded during phase 2 assembly of clustered reads

Fantastic! I always love hearing about when things work! :-) all the best, Brian On Thu, Nov 30, 2023

11/30/23

Neeraja Balasubrahmaniam, Brian Haas5

11/21/23

Pearson Correlation- Differential Expression Analysis

Oh, I see. I thought you were running this: https://github.com/trinityrnaseq/trinityrnaseq/wiki/QC-

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Pearson Correlation- Differential Expression Analysis

Oh, I see. I thought you were running this: https://github.com/trinityrnaseq/trinityrnaseq/wiki/QC-

11/21/23

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