I'm trying to assemble some transcriptomes using Trinity, but am having issues getting Trinity to finish. I've been trying to get this to work for weeks, but am hitting a wall and would very much appreciate any and all help.
I have 2 treatment conditions, with 3 replicates per condition, and they were sequenced on a NovaSeq (using 2x150 base reads). I originally tried assembling all the samples together, but even after running for 8+ days it did not finish.
I am now trying to run just 1 sample from each condition, but even after 4 days Trinity will not finish. It seems like it is stuck at Butterfly, and I'm unsure how to proceed. Some more detail and things I've tried:
These are microbial isolates grown in axenic culture, not metagenomic samples. The microbes are protists though (not bacteria), so their transcriptomes are more complex than prokaryotes, but not as complex as higher eukaryotes like humans/mice.
I do not need to have high sensitivity for lowly expressed transcripts, so I tried setting the "min_kmer_cov" higher. First I set it to 2, which did not help. Then I tried 10 (seemed extreme but I was desperate, but even that has not solved it).
-I am running these on a cluster, and admittedly I am not knowledgeable at all about how to optimally request resources, so I am wondering if that is part of the issue. Our cluster uses slurm, and my resource requests right now are
#SBATCH --mem 100000 #SBATCH -n 24 #SBATCH -N 6".
-I tried running just one replicate from one of my conditions. This did finish (after ~42 hours), so it seems like the issue is not an inherent problem with the transcriptomes/the data itself.
Thank you very much!
By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. This approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.
Trinity Trinity is a de novo assembler that fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes using de Bruijn graphs. Trinity recover full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments.