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Hi,
I'm trying to combine my TACO output and TD output within this command but it returns error:
`$TD_PATH/util/cdna_alignment_orf_to_genome_orf.pl longest_orfs.cds.transdecoder.gff3 ../TACO/out…
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Hello everyone
While running autoTrinotate.pl I got this error after 2 days of hmmscan run:
```
* Running CMD: hmmscan --cpu 22 --domtblout TrinotatePFAM.out /mnt/beegfs/manoud/aa_assembly_run4…
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Hi all!
I am trying to combine the files below:
1. `masked.A.gff` from **directly runing AUGUSTUS with genome file** and converting by `augustus_GFF3_to_EVM_GFF3.pl`;
2. `augustus.hints.B.gtf` fr…
wu116 updated
12 months ago
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Hi,
After we called variants using the GATK pipeline, is there a way to annotate the variants as synonymous or non-synonymous using ORF annotations generated by Transdecoder?
Thank you so much!
Shu
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Hi brian,
can I change following into
-outfmt 6 -evalue 1e-3 > blastp.outfmt6
this
-outfmt 7 -evalue 1e-3 > blastp.outfmt7
because in same directory I already have blastp.outfmt6 file from Tr…
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I did trinity assembly and then polished it using TransDecoder and cd-hit. Then I run the downstream analysis using `align_and_estimate_abundance.pl`, but got the following error:
```
Mapping Info…
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Hello,
I'm trying to use EVM to combine two things:
- output of BRAKER1 which used GeneMark **and Augustus trained with RNA-seq data** (BAM alignment file of the RNA-seq to the (masked) genome). I…
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Hi!
I keep getting the error below while trying to run the autoTrinotate.pl script for my Trinity-assembled transcriptome (fasta file).
Any advice on where the issue may lie would be greatly ap…
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I'm working on integrating this into my VEBA pipeline (github.com/jolepsin/veba) and will be running multiple instances of this at the same time. I can't do that when the final files are output into t…
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I'm getting segmentation faults thrown with one transcriptome, tried running both blastx and blastp and both fail. See here for the files:
https://drive.google.com/file/d/1v2f7wH-6G4MvFERaaZ96aDeFJjT…