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Hello,
Curious if the 5'prime partial ORFs, which lack start codon (M), should be considered for the downstream analyses?. Also, is it preferable to consider only the longest ORFs per gene/transcript…
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My goal is to create a genome guided transcriptome assembly using Stringtie and use gffread to convert the output GFT into a GFF3. I seem to be able to create the .gff3 file without a problem, but I w…
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Hello. I'm getting the following error, but I'm not sure how to debug it:
```
Mikado crashed, cause:
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/Mikado/__ma…
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Hi Brian,
Thank you for providing such wonderful tool. I am new with PASA, and want to use it for both alignment assembly and annotation update.
For the alignment assembly section, I have three …
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Hi,
I'm trying to use Trinotate for different datasets and I'm stuck on the last step. When I generate the report I get the error below that I don't understand (for each of my datasets it processes…
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After getting dammit and all of the dependencies installed onto my Ubuntu machine, I tried following the annotation tutorial with the sample data, but the program failed after about four hours with t…
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Hi there,
I've been trying to use TransPi (love the concept and the benchmarking in the paper looks great!) to re-assemble some older public datasets. Running on an interactive slurm session of an …
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@ljcohen has some code, maybe... :)
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Hello!
I now have RNA-seq data and full-length transcriptome data from several tissues, and I used "Trinity genome-guieded" to get the transcript "Trinity-GG.fasta" of the RNA-seq . At the same time,…
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Convert `transcriptome_annotated.pep` to CSV format as it is more convenient to import in pandas. As discussed with @tomas-pluskal, it makes little sense for the pipeline to first create the `transcri…