Questions tagged [trinity]

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Trinity de novo transcriptome assembly: samtools view failed to add PG line to the header

I have assembled the transcriptome a plant species using Trinity. Here is the command: ...
Faroll's user avatar
  • 11
2 votes
1 answer

Trinity de novo assembly not completing

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 ...
egerr's user avatar
  • 21
1 vote
2 answers

Remove variable sequence component within a tree text file

I have a gene tree file of 436 orthologue genes from 6 species. I want to remove unwanted extensions as it looks massy after visualization. My file looks like: (TRINITY_Clupea_DN5452_c0_g1_i1.p1:0....
Kishor Kumar Sarker's user avatar
0 votes
1 answer

Trinity Multi-species compatibility

I am using Trinity from last couple-up months or so. Initially, using same species in different condition was worked fine for me. Now i am trying to do a DE analysis using multiple species. Actually, ...
Kishor Kumar Sarker's user avatar
1 vote
1 answer

Assembling all transcripts for an individual gene? (using single sequence to seed the assembly)

Let's say I have a candidate gene and I believe that in an individual sample, the genome sequence differs from the reference which then interferes with alignment. Is there a way for me to do a "...
story's user avatar
  • 1,568