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Maybe it possible to change the directory where Transrate writes the final output? By now it's the working directory and, in my opinion it'd be a good idea change that and write the final output in th…
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Hi Brian,
How can we retain those transcripts if transcripts were not predicted to contain a protein-coding ORF (using blast and pfam), as long as they meet the minimum transcript length?
Also h…
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I have used e-training to establish my own species model. However, according to the manual "Incorporating RNA-Seq into AUGUSTUS", it uses blat2hints.pl getting the information of intron. I don't know …
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Hi,
Can't complete the pipeline. I get an error.
```
executor > local (27)
[15/32ba1b] process > fasqc (reads_R) [100%] 1 of 1 ✔
[c5/32f96c] process > fastp (reads_R) …
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HI,
> If you have RNA-Seq data and have reconstructed transcripts using a method such as [Cufflinks](http://cole-trapnell-lab.github.io/cufflinks/) or [PASA](http://pasapipeline.github.io/), you ca…
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Transdecoder by default dumps the final output files into the current directory, regardless of output folder settings.
Should figure out how to change this behavior using TransDecoder or just mv the …
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Hi Lars,
My team has recently curated over 20k genes for a novel Caenorhabditis genome we have assembled. I noticed that we underperform in sensitivity relative to TSEBRA annotations (generated by …
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Dear Brian,
For my RNAseq experiment, I would like to use the predicted transcripts for the genome of my organism as a transcriptome reference. To do a GO enrichment analysis, I was thinking of an…
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Hi, there.
Since I have used the stringtie merge parameters to combined all the gtf file together. As we can see that there are just the transcripts and exons features in the final files.
![imag…
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Hi I am writing to consult the reason of an erroneous GFF file checked by "_gff3_gene_prediction_file_validator.pl_".
This GFF file "**isoseq_all_four_tissues.fastq.transcript_models_IDfixed.gff**"…