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@thardy615 - Hi Tanjanay,
I got my github credentials working again, and just checked in
````
TrenaProjectArabidopsisRoot/explore/dataFrameRowExpansion/paulsSuggestion/rowExpansion.R
````
T…
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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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Dear authors,
I've a question related to the procedure that you followed to classify translated and untranslated ORFs after finishing running ORQAS. How do you exactly determine the cut-off values …
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I searched for a particular ORF sequence against a given database, using ssearch36.
```fasta36 -E 10 -f 10 -g 2 orf.fasta library.fasta 2```
Then I searched for a multi-FASTA file containing man…
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When running example control file, the Glimmer extract stage fails because the following files are not produced:
- MMAP_example.glimmer.detail
- MMAP_example.glimmer.predict
However, glimmer extract …
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Hi there,
I as hoping someone could help me, I a**m trying to initialize my Trinotate sqlite database using this code:**
perl /home/ubuntu/miniconda3/envs/trinotate/bin/Trinotate Trinotate.sqlit…
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Hi there,
Should I specify an evalue for the hmmscan for Including homology searches as ORF retention criteria? In the tutorial, you didn't specify a evalue: `hmmsearch --cpu 8 --domtblout pfam.dom…
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Hi @hyeshik ,
First of all, thanks much for your efforts and this neat, thorough and transparent work.
I managed to run the *reference* snakemake workflow, but for the *nanopore* workflow there we…
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Hello,
I was wondering if there is a way to further break down ORF annotations presented by the ribotricer algorithm.
I would like to get a sense for proportion of different non-canonical OR…
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Hello,
I've been a big fan of TElocal, especially for its clear definitions of complicated TE system. As someone from other fields, I always feel some sort of disconnection between mainstream TE re…