trinityrnaseq-users

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Roger that, thanks very much for your help as always, Brian. --Robert On Friday, November 17, 2023 at

Dear TrinityRNASeqUsers community, I began an assembly yesterday with nine paired-end libraries that

Hi i am currently working on single cell transcriptome assembly and i hope to keep as much as contigs

I'm pretty sure I just removed the 'wrong' singularity. Since I installed it using '

Greetings all, Some of you were encountering a gstrand bit error with STAR. To address this, please

Hi all! All of our Trinity de novo assembly funding comes from the National Cancer Institute, and all

Hi, There's a script at: trinityrnaseq/util/misc/fasta_filter_by_min_length.pl fastaFile