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Welcome to the Trinity de novo RNA-Seq assembly user list! :)
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Holly Williams
,
Brian Haas
2
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
Shoyo Sato
Mar 21
inchworm error
Hello! I'm running trinity on multiple samples with an array job and I seem to be having issues
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inchworm error
Hello! I'm running trinity on multiple samples with an array job and I seem to be having issues
Mar 21
Hu Wang
, …
Janay Fox
3
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 Haas
3
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 Kunselman
2
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
Jake Nash
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
Janay Fox
2
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
Janay Fox
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 Jovović
5
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
Trinity Error
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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Trinity Error
Dear Trinity users, I have tried to run trinity file for de novo seq assembly. I got an error which i
Feb 15
Lada Jovović
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 Haas
2
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 Haas
4
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 Haas
4
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 Haas
2
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
Nishant Raj
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 Haas
9
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 Haas
2
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 Haas
2
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 Haas
6
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 Haas
5
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
Rob W.
,
Brian Haas
7
11/20/23
Jellyfish Pipeliner.pm line 187 error: no such file or directory
Roger that, thanks very much for your help as always, Brian. --Robert On Friday, November 17, 2023 at
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Jellyfish Pipeliner.pm line 187 error: no such file or directory
Roger that, thanks very much for your help as always, Brian. --Robert On Friday, November 17, 2023 at
11/20/23
Adrián Esteban Velázquez Lizárraga
11/15/23
Jellyfish is taking too long
Dear TrinityRNASeqUsers community, I began an assembly yesterday with nine paired-end libraries that
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Jellyfish is taking too long
Dear TrinityRNASeqUsers community, I began an assembly yesterday with nine paired-end libraries that
11/15/23
sernyan lim
11/14/23
Am i able to run Trinity with min_con_length below 100
Hi i am currently working on single cell transcriptome assembly and i hope to keep as much as contigs
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Am i able to run Trinity with min_con_length below 100
Hi i am currently working on single cell transcriptome assembly and i hope to keep as much as contigs
11/14/23
Olivia Wynn
,
Brian Haas
3
11/1/23
Crash bug: can't get singularity to bind/execute my trinity image. singularity command responds with the same warning message - core dumped
I'm pretty sure I just removed the 'wrong' singularity. Since I installed it using '
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Crash bug: can't get singularity to bind/execute my trinity image. singularity command responds with the same warning message - core dumped
I'm pretty sure I just removed the 'wrong' singularity. Since I installed it using '
11/1/23
Brian Haas
10/27/23
Announcement: CTAT genome libs for STAR v2.7.11a - solve gstrand bit error?!?
Greetings all, Some of you were encountering a gstrand bit error with STAR. To address this, please
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Announcement: CTAT genome libs for STAR v2.7.11a - solve gstrand bit error?!?
Greetings all, Some of you were encountering a gstrand bit error with STAR. To address this, please
10/27/23
Brian Haas
10/12/23
Trinity Cancer Researchers ** Please Read**
Hi all! All of our Trinity de novo assembly funding comes from the National Cancer Institute, and all
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Trinity Cancer Researchers ** Please Read**
Hi all! All of our Trinity de novo assembly funding comes from the National Cancer Institute, and all
10/12/23
sumitra sivaprakasam
,
Brian Haas
2
10/12/23
Removing contigs <200bp
Hi, There's a script at: trinityrnaseq/util/misc/fasta_filter_by_min_length.pl fastaFile
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Removing contigs <200bp
Hi, There's a script at: trinityrnaseq/util/misc/fasta_filter_by_min_length.pl fastaFile
10/12/23